Taxonomy of Protista

A protist is any eukaryotic organism (one with cells containing a nucleus) that is not an animal, plant, or fungus. The protists do not form a natural group, or clade, since they exclude certain eukaryotes with whom they share a common ancestor; but, like algae or invertebrates, the grouping is used for convenience. In some systems of biological classification, such as the popular five-kingdom scheme proposed by Robert Whittaker in 1969, the protists make up a kingdom called Protista, composed of "organisms which are unicellular or unicellular-colonial and which form no tissues". In the 21st century, the classification shifted toward a two-kingdom system of protists: Chromista (containing the chromalveolate, rhizarian and hacrobian groups) and Protozoa (containing excavates and all protists more closely related to animals and fungi).

The following groups contain protists. The clade Opisthokonta also contains the animals and the fungi, and the kingdom Archaeplastida also contains algae and plants.

Key to symbols used:
 * (P) = Paraphyletic group.
 * † = Extinct group.
 * ? = Group of uncertain taxonomic position.
 * * = Group lacking molecular data.
 * [ ] = Synonyms and alternative names.

Current classification
This article largely follows the efforts of the scientific community and the International Society of Protistologists to revise the taxonomy of protists in a manner that reflects their phylogeny and evolution, striving away from the use of historical paraphyletic taxa and relying exclusively on clades as the basis of the classification. The reference used for the general arrangement of groups is the publication Revisions to the Classification, Nomenclature and Diversity of Eukaryotes, published in 2019 by researcher Sina Adl and coauthors. Other studies are used for some specific groups of protists that have been revised after 2018, such as slime moulds, glaucophyte algae, arcellinid testate amoebae and planktonic foraminifera.

The following cladogram shows the relationships between the major groups of protists, as well as the kingdoms of animals, plants and fungi, according to the most recent phylogenetic analyses.

Obazoa {{au|Brown et al. 2013}}
Incertae sedis Obazoa:
 * Apusomonadida [Apusomonadidae ; Thecomonadea ]. Amastigomonas, Apusomonas, Chelonemonas, Manchomonas, Multimonas, Podomonas, Thecamonas, Catacumbia, Cavaliersmithia, Karpovia, Singekia.
 * Breviatea [Breviatida ; Breviatidae ]. Breviata, Lenisia, Pygsuia, Subulatomonas.

Opisthokonta {{au|Cavalier-Smith 1987, emend. Adl et al. 2005}}

 * Nucletmycea [Holomycota ]
 * Rotosphaerida [Cristidiscoidida ; Nucleariidae ]. Fonticula, Nuclearia, Parvularia, Pompholyxophrys, Lithocolla, ?Vampyrellidium*, ?Elaeorhanis*, ?Pinaciophora*, ?Rabdiophrys*, ?Rabdiaster*, ?Thomseniophora*.
 * Fungi . Excluded from protists.
 * Holozoa . Incertae sedis: Tunicaraptor, Bicellum.
 * Ichthyosporea [Mesomycetozoea ]
 * Dermocystida [Rhinosporidaceae ]. Amphibiocystidium, Amphibiothecum, Chromosphaera, Dermocystidium, Rhinosporidium, Sphaerothecum.
 * Ichthyophonida [Ichthyophonae ; Amoebidiidae ]. Abeoforma, Amoebidium, Anurofeca, Astreptonema, Caullerya, Creolimax, Eccrinidus, Enterobryus, Enteropogon, Ichthyophonus, Palavascia, Pseudoperkinsus, Psorospermium, Sphaeroforma.
 * Pluriformea
 * Corallochytrium
 * Syssomonas
 * Filasterea . Capsaspora, Ministeria, Pigoraptor, Txikispora.
 * Choanozoa [Choanozoa  (P)]
 * Choanoflagellata [Craspedomonadina ; Craspedomonadaceae ; Craspedophyceae ; Craspédomonadophycidées ; Craspedomonadophyceae ; Choanomonadea ; Choanoflagelliida ; Choanoflagellatea ; Choanomonada ].
 * Craspedida
 * Salpingoecidae . Astrosiga, Aulomonas, Choanoeca, Cladospongia, Codonocladium, Codonosigopsis, Codosiga [Codonosiga], Desmarella [Codonodesmus; Kentrosiga], Dicraspedella, Diploeca, Diplosiga, Diplosigopsis, Hartaetosiga, Kentia, Lagenoeca, Microstomoeca, Monosiga, Mylnosiga, Pachysoeca, Proterospongia, Salpingoeca, Salpingorhiza, Sphaeroeca, Stagondoeca, Stelexomonas, Stylochromonas.
 * Acanthoecida
 * Acanthoecidae . Acanthoeca, Enibas, Helgoeca, Polyoeca, Savillea.
 * Stephanoecidae . Acanthocorbis, Amoenoscopa, Apheloecion, Bicosta, Calliacantha, Calotheca, Campanoeca, Campyloacantha, Conion, Cosmoeca, Crinolina, Crucispina, Diaphanoeca, Didymoeca, Kakoeca, Monocosta, Nannoeca, Parvicorbicula, Platypleura, Pleurasiga, Polyfibula, Saepicula, Saroeca, Spinoeca, Spiraloecion, Stephanacantha, Stephanoeca, Syndetophyllum.
 * Metazoa [Animalia ; Eumetazoa ]. Excluded from protists.

Amoebozoa {{au|Lühe 1913, sensu Cavalier-Smith 1998}}
Incertae sedis Amoebozoa: Belonocystis, Boveella, Biomyxa, Corallomyxa, Gibbodiscus, Hartmannia, Malamoeba, Malpighamoeba, Microglomus, Oscillosignum, Pseudothecamoeba, Rhabdamoeba, Schoutedamoeba, Stereomyxa, Subulamoeba, Thecochaos, Triaenamoeba, Unda.

Tubulinea {{au|Smirnov et al. 2005}}

 * Corycida Kang et al. 2017 ["Corycidia"]
 * Trichosida [Trichosphaeriidae ]. Trichosphaerium.
 * Microcoryciidae . Amphizonella, Diplochlamys, Trichosphaerium [Atrichosa], Microcorycia*, Parmulina*, Penardochlamys*, Zonomyxa*.
 * Echinamoebida Cavalier-Smith 2004.
 * Echinamoebidae Page 1975. Echinamoeba, Micriamoeba.
 * Vermamoebidae Cavalier-Smith & Smirnov 2011. Vermamoeba.
 * Elardia
 * Leptomyxida Pussard & Pons 1976 sensu Page 1987
 * Leptomyxidae Pussard & Pons 1976. Leptomyxa.
 * Rhizamoebidae Smirnov et al. 2016. Rhizamoeba.
 * Flabellulidae Bovee 1970. Flabellula [incl. Paraflabellula].
 * Gephyramoebidae Pussard & Pons 1976. Gephyramoeba.
 * Arcellinida Kent 1880. Incertae sedis genera: Acipyxis, Apolimia, Argynnia, Armipyxis, Conicocassis, Cornuapyxis, Ellipsopyxella, Ellipsopyxis, Erugomicula, Frenopyxis, Geamphorella, Geoplagiopyxis, Geopyxella, Hoogenraadia, Jungia, Lagenodifflugia, Lamptopyxis, Lamptoquadrula, Leptochlamys, Maghrebia, Meisterfeldia, Microquadrula, Nabranella, Oopyxis, Paracentropyxis, Paraquadrula, Pentagonia, Physochila, Planhoogenraadia, Pomoriella, Pontigulasia, Prantlitina, Proplagiopyxis, Protoplagiopyxis, Protocucurbitella, Pseudawerintzewia, Pseudonebela, Schoenbornia, Sexangularia, Suiadifflugia, Trigonopyxis, Wailesella.
 * Phryganellina Bovee 1985
 * Phryganellidae Jung 1942. Phryganella.
 * Cryptodifflugiidae Jung 1942. Cryptodifflugia.
 * Organoconcha Lahr et al. 2019
 * Microchlamyiidae Ogden 1985. Microchlamys, Spumochlamys, Pyxidicula.
 * Glutinoconcha Lahr et al. 2019
 * Volnustoma Lahr et al. 2019
 * Heleoperidae Jung 1942. Heleopera.
 * Hyalospheniformes Lahr et al. 2019
 * Hyalospheniidae Schultze 1877 emend. Kosakyan et al. 2012. Alabasta, Alocodera, Apodera, Certesella, Cornutheca, Gibbocarina, Hyalosphenia, Longinebela, Mrabella, Nebela, Padaungiella, Planocarina, Porosia, Quadrulella.
 * Excentrosoma Lahr et al. 2019
 * Centropyxidae Jung 1942 [includes Plagiopyxidae]. Awerinzewia, Bullinularia, Centropyxis, Golemanskia, Plagiopyxis.
 * Cylindrothecina González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022
 * Cylindrifflugiidae González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022. Cylindrifflugia.
 * Longithecina Lahr et al. 2019
 * Difflugiidae Wallich 1864. Difflugia, Zivkovicia.
 * Lesquereusiidae Jung 1942. Lesquereusia.
 * Sphaerothecina Kosakyan et al. 2016
 * Arcellidae Ehrenberg 1843. Arcella, Galeripora.
 * Netzeliidae Kosakyan et al. 2016. Cucurbitella, Cyclopyxis, Netzelia
 * Euamoebida Lepşi 1960 sensu Smirnov et al. 2011
 * Amoebina Cavalier-Smith 2016
 * Amoebidae Ehrenberg 1838 Page 1987. Amoeba, Chaos, Polychaos, Parachaos, Trichamoeba, Deuteramoeba, Hydramoeba
 * Hartmannellidae Volkonsky 1931. Cashia, Copromyxa, Copromyxella, Glaeseria, Hartmannella, Ptolemeba, Saccamoeba
 * Nolandina Cavalier-Smith 2016
 * Nolandellidae Cavalier-Smith 2011, Lahr & Katz 2011. Nolandella.

Evosea {{au|Kang et al. 2017}}

 * Variosea Cavalier-Smith 2004
 * Angulamoeba
 * Arboramoeba
 * Darbyshirella
 * Dictyamoeba
 * Ischnamoeba
 * Heliamoeba
 * Filamoeba
 * Phalansterium.
 * Flamellidae . Flamella, Telaepolella.
 * Protosteliida . Protostelium [incl. Planoprotostelium].
 * Fractovitellida
 * Acramoebidae . Acramoeba.
 * Schizoplasmodiidae . Ceratiomyxella, Nematostelium, Schizoplasmodium.
 * Soliformoviidae . Soliformovum, Grellamoeba
 * Cavosteliida . Cavostelium, Schizoplasmodiopsis, Tychosporium.
 * Holomastigida Lauterborn 1895. Artodiscus, Multicilia.
 * Eumycetozoa [Mycetozoa de Bary 1859 ex Rostafinski 1873; Macromycetozoa ]
 * Dictyostelia Lister 1909 sensu Sheikh et al. 2018 [Dictyosteliomycetes Doweld 2001]. Acytostelium, Cavenderia, Coremiostelium, Dictyostelium, Heterostelium, Polysphondylium, Raperostelium, Rostrostelium, Speleostelium, Tieghemostelium, Synstelium, ?Coenonia.
 * Protosporangiida Shadwick & Spiegel in Adl et al. 2012 [Ceratiomyxea Leontyev, Stephenson, Novozhilov & Shchepin 2019; Ceratiomyxomycetes D. Hawksw., B. Sutton & Ainsw. 2019]
 * Ceratiomyxa
 * Protosporangiidae . Clastostelium, Protosporangium.
 * Myxogastria [Myxogastrea Cavalier-Smith 1993; Myxomycetes Link 1833, sensu Haeckel 1866]
 * Lucisporomycetidae [Lucisporinia Leontyev, Stephenson, Novozhilov & Shchepin 2019; Lucisporidia ]. Incertae sedis genera: Arcyriatella, Calonema, Minakatella, Trichioides.
 * Cribariidia Leontyev, Stephenson, Novozhilov & Shchepin 2019
 * Cribariales T. Macbr. 1922
 * Cribariaceae Corda 1838. Cribaria, Lindbladia, Licaethalium.
 * Trichiidia Leontyev, Stephenson, Novozhilov & Shchepin 2019
 * Reticulariales Leontyev, Stephenson, Novozhilov & Shchepin 2019
 * Reticulariaceae Chevall. 1842. Alwisia, Lycogala, Reticularia, Tubifera.
 * Liceales E. Jahn 1928
 * Liceaceae Chevall. 1826. Licea, Listerella.
 * Trichiales T. Macbr. 1922
 * Dianemataceae T. Macbr. 1922. Calomyxa, Dianema, Dictydiaethalium, Prototrichia.
 * Trichiaceae Chevall. 1826 sensu Martin & Alexopoulos 1969. Hemitrichia [incl. Trichia decipiens], Arcyria [incl. Arcyodes], Perichaena, Trichia [incl. Cornuvia, Metatrichia, Oligonema].
 * Columellomycetidae [Collumellinia Leontyev, Stephenson, Novozhilov & Shchepin 2019; Columellidia ]. Incertae sedis genera: Diachea, Echinosteliopsis, Leptoderma, Paradiachea, Protophysarum, Trabrooksia, Willkommlangea.
 * Echinosteliidia Leontyev, Stephenson, Novozhilov & Shchepin 2019
 * Echinosteliales G. W. Martin 1961
 * Echinosteliaceae Rostaf. ex Cooke 1877. Barbeyella, Echinostelium [incl. Semimorula].
 * Stemonitidia Leontyev, Stephenson, Novozhilov & Shchepin 2019
 * Clastodermatales Leontyev, Stephenson, Novozhilov & Shchepin 2019
 * Clastodermataceae Alexop. & T.E. Brooks 1971. Clastoderma.
 * Meridermatales Leontyev, Stephenson, Novozhilov & Shchepin 2019
 * Meridermataceae Leontyev, Stephenson, Novozhilov & Shchepin 2019. Meriderma.
 * Stemonitidales T. Macbr. 1922 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019
 * Stemonitidaceae Fr. 1829 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019. Macbrideola, Stemonitis, Symphytocarpus.
 * Amaurochaetaceae Rostaf. ex Cooke 1877 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019. Comatricha, Stemonaria, Stemonitopsis, Amaurochaete, Brefeldia, Enerthenema, Paradiacheopsis.
 * Physarales T. Macbr. 1922
 * Tasmaniomyxa umbilicata
 * Lamprodermataceae T. Macbr. 1899 em. Leontyev, Stephenson, Novozhilov & Shchepin 2019. Lamproderma [incl. Dichaeopsis, Colloderma, Elaeomyxa], ?Collaria.
 * Didymiaceae Rostaf. ex Cooke 1877 – Diderma, Didymium, Lepidoderma, Mucilago.
 * Physaraceae Chevall. 1826. Craterium, Leocarpus, Fuligo, Physarum, Physarella, Physarina, Kelleromyxa, Badhamia.
 * Cutosea Cavalier-Smith 2016 [Squamocutida Cavalier-Smith 2016]
 * Squamamoebidae Cavalier-Smith 2016. Armaparvus, Squamamoeba.
 * Sapocribridae Cavalier-Smith 2016. Sapocribrum.
 * Idionectidae . Idionectes.
 * Archamoebea
 * Tricholimacidae . Tricholimax.
 * Entamoebidae . Entamoeba.
 * Rhizomastixidae . Rhizomastix.
 * Mastigamoebida . Endamoeba, Endolimax, Iodamoeba, Mastigamoeba, Mastigina.
 * Pelobiontida Page 1976, sensu Cavalier-Smith 2013 [Pelomyxidae ]. Mastigella, Pelomyxa

Discosea {{small|Cavalier-Smith et al. 2004 sensu Smirnov et al. 2011}}

 * Flabellinia Smirnov et al. 2005
 * Dermamoebida
 * Dermamoebidae Cavalier-Smith & Smirnov 2011. Dermamoeba, Paradermamoeba, ?Mycamoeba, Coronamoeba.
 * Mayorellidae Schaeffer 1926. Mayorella.
 * Thecamoebida . Sappinia, Stenamoeba, Stratorugosa, Thecamoeba, Thecochaos.
 * Dactylopodida . Cunea, ?Janickina,* Korotnevella, Neoparamoeba, Paramoeba, Pseudoparamoeba, Vexillifera.
 * Vannellida [Vannellidae ]. Clydonella, Lingulamoeba, Paravannella, Pessonella*, Ripella, Vannella.
 * Stygamoebida Smirnov & Cavalier-Smith in Smirnov et al. 2011 (P). Stygamoeba, Vermistella.
 * Centramoebia
 * Acanthopodida [Centramoebida  ]. Acanthamoeba, Balamuthia, Luapeleamoeba, Protacanthamoeba, Dracoamoeba, Vacuolamoeba.
 * Himatismenida . Cochliopodium, Ovalopodium, Parvamoeba.
 * Pellitida . Endostelium, Gocevia, Paragocevia*, Pellita.

Diaphoretickes {{au|Adl et al. 2012}}

 * Microheliella maris
 * Telonemia [Telonemidae ]. Arpakorses, Lateronema, Telonema.
 * Provora
 * Nibbleridia . Nibbleromonas, Ubysseya.
 * Nebulidia . Nebulomonas, Ancoracysta.

Archaeplastida {{au|Adl et al. 2005}}

 * Glaucophyta [Glaucocystaceae ; Glaucocystophyta ]. Incertae sedis Glaucophyta: ?Archaeopsis, ?Chalarodora, ?Glaucocystopsis, ?Peliaina, ?Strobilomonas.
 * Cyanophorales . Cyanophora.
 * Glaucocystales . Glaucocystis.
 * Gloeochaetales . Cyanoptyche, Gloeochaete.
 * Picozoa [Picobiliphytes ]. Picomonas.
 * Rhodelphidia . Rhodelphis.
 * Rhodophyceae [Rhodophyta ; Rhodoplantae ]
 * Chloroplastida [Viridiplantae ; Chlorobionta ; Chlorobiota ]

Stramenopiles {{au|Patterson 1989, emend. Adl et al. 2005}}
Stramenopiles incertae sedis:
 * Environmental clades MAST-21, MAST-25
 * Platysulcidae . Platysulcus.
 * Kaonashiidae . Kaonashia.

Bigyra {{au|Cavalier-Smith 1998, emend. 2006}}

 * Opalozoa . Incertae sedis: Cantina, Rictus, environmental clades MAST-16, MAST-22 and MAST-24.
 * Placidozoa
 * Placididea . Allegra, Haloplacidia, Pendulomonas, Placidia, Placilonga, Suigetsumonas, Wobblia.
 * Nanomonadea [clade MAST-3]. Incisomonas, Solenicola.
 * Opalomonadea [clade MAST-12]. No described species.
 * Opalinata [Slopalinida ]
 * Proteromonadea . Karotomorpha, Proteromonas.
 * Opalinea . Cepedea, Opalina, Protoopalina, Protozelleriella, Zelleriella.
 * Blastocystis
 * Bicosoecida . Adriamonas, Anoeca, Bicosoeca, Caecitellus, Cafeteria, Cafileria, Cyathobodo, Filos, Halocafeteria, Nanum, Paramonas, Pseudobodo, Pseudodendromonas, Otto, Regin.
 * Sagenista . Incertae sedis: environmental clades MAST-4, MAST-7, MAST-8, MAST-9, MAST-10, MAST-11 and MAST-20.
 * Labyrinthulomycetes
 * Amphitremida . Amphitrema, Archerella, Diplophrys, Paramphitrema.
 * Amphifilida . Amphifila, Fibrophrys, Sorodiplophrys.
 * "Oblongichytrida" . Oblongichytrium.
 * Labyrinthulida . Aplanochytrium, Labyrinthula, Stellarchytrium.
 * Thraustochytrida . Althornia, Aurantiochytrium, Botryochytrium, Japanochytrium, Monorhizochytrium, Parietichytrium, Phycophthorum, Schizochytrium, Sicyoidochytrium, Thraustochytrium, Ulkenia.
 * Pseudophyllomitidae [clade MAST-6]. Pseudophyllomitus.

Gyrista {{au|Cavalier-Smith 1998}}

 * Gyrista incertae sedis: environmental clades MAST-1, MAST-2 and MAST-23.
 * Bigyromonadea
 * Developea . Developayella, Develorapax.
 * Pirsoniales . Pirsonia.
 * Pseudofungi [Heterokontimycotina ].
 * Hyphochytriales . Anisolpidium, Canteriomyces.
 * Anisolpidiaceae
 * Hyphochytridiomycetaceae . Hyphochytrium.
 * Rhizidiomycetaceae . Latrostium, Rhizidiomyces, Rhizidiomycopsis.
 * Oomycetes [Peronosporomycetes ]. Incertae sedis genera: Atkinsiella, Ciliomyces, Crypticola, Ectrogella, Eurychasma, Halodaphnea, Haliphthoros, Haptoglossa, Lagena, Lagenisma, Olpidiopsis, Pontisma, Pythiella, Rozellopsis, Sirolpidium.
 * Saprolegnialean lineage . Achlya, Aphanomyces, Aplanopsis, Apodachlya, Aquastella, Geolegnia, Leptomitus, Newbya, Pythiopsis, Protoachlya, Salisapilia, Saprolegnia, Thraustotheca.
 * Peronosporalean lineage . Albugo, Bremia, Chlamydomyzium, Halophytopthora, Hyaloperonospora, Lagenidium, Myzocytiopsis, Peronospora, Plasmopara, Pythium, Pseudoperonospora, Phytophthora, Phytopythium, Pustula.
 * Ochrophyta
 * Chrysista . Incertae sedis: environmental lineages MOCH-3 and MOCH-5, Chrysowaernella, Aurearena.
 * SII clade
 * Olisthodiscophyceae . Olisthodiscus.
 * Pinguiophyceae . Glossomastix, Phaeomonas, Pinguiochrysis, Pinguiococcus, Polypodochrysis.
 * Limnistia
 * Chrysophyceae . Incertae sedis: Chryososaccus, Chrysosphera, Cyclonexis, Lygynion, Phaeoplaca.
 * Chromulinales . Chromulina, Chrysomonas.
 * Hibberdiales . Hibberdia.
 * Ochromonadales . Spumella, Pedospumella, Ochromonas.
 * Paraphysomonadida . Paraphysomonas.
 * Synurales . Chrysodidymus, Mallomonas, Synura, Tesselaria.
 * Eustigmatophyceae
 * Eustigmatales
 * Paraeustigmatos
 * Eustigmataceae . ?Ellipsoidion, Chlorobotrys, Eustigmatos, Pseudocharaciopsis, Vischeria.
 * Monodopsidaceae . Microchloropsis, Monodopsis, Nannochloropsis, Pseudotetraedriella.
 * Neomonodaceae . ?Botryochloropsis, Characiopsella, Munda, Neomonodus, Pseudellipsoidion.
 * Goniochloridales . Goniochloris, Pseudostaurastrum, Tetraedriella, Trachydiscus, Vacuoliviride.
 * Picophagea [Synchromophyceae ]. Chlamydomyxa, Chrysopodocystis, Guanochroma, Leukarachnion, Picophagus, Synchroma.
 * SI clade
 * Raphidomonadea
 * Raphidophycidae [Chattonellales ; Vacuolariales ]. Chattonella, Fibrocapsa, Goniostomum, Haramonas, Heterosigma, Merotricha, Vacuolaria.
 * Raphopoda
 * Commatiida [Commatiidae ]. Commation.
 * Actinophryida
 * Actinosphaerina [Actinosphaeriidae ]. Actinosphaerium.
 * Actinophryina
 * Actinophryidae . Actinophrys.
 * Helioraphidae . Heliorapha.
 * PX clade
 * Chrysomerophyceae . Antarctosaccion, Chrysomeris, Chrysowaernella, Giraudyopsis, Rhamnochrysis, Tetrasporopsis.
 * Chrysoparadoxophyceae . Chrysoparadoxa.
 * Phaeophyceae
 * Ascoseirales . Ascoseira.
 * Desmarestiales . Arthrocladia, Desmarestia (P), Himantothallus, Phaeurus.
 * Dictyotales . Dictyota, Dilophus, Lobophora, Padina, Stypopodium, Taonia, Zonaria.
 * Discosporangiales . Choristocarpus, Discosporangium.
 * Ectocarpales . Adenocystis, Acinetospora, Asterocladon, Asteronema, Chordaria, Ectocarpus, Scytosiphon.
 * Fucales . Ascophyllum, Bifurcaria, Cystoseira, Druvillaea, Fucus, Hormosira, Sargassum, Turbinaria.
 * Ishigeales [Ishigeacea ]. Ishige.
 * Laminariales . Akkesiophycus, Alaria, Chorda, Costaria, Laminaria, Lessonia, Pseudochoda.
 * Nemodermatales . Nemoderma.
 * Onslowiales . Onslowia.
 * Ralfsiales . Lithoderma, Neoralfsia, Pseudolithoderma, Ralfsia.
 * Scytothamnales . Scytothamnus, Splachnidium, Stereocladon.
 * Sphacelariales . Chaetopteris, Halopteris, Stypocaulon, Sphacelaria, Verosphacella.
 * Sporochnales . Bellotia, Carpomitra, Nereia, Sporochonus, Tomaculopsis.
 * Syringodermatales . Syringoderma.
 * Tilopteridales . Cutleria, Halosiphon, Haplospora, Phaeosiphoniella, Phyllaria, Tilopteris.
 * Phaeosacciophyceae
 * Phaeosaccionaceae . Phaeosaccion.
 * Tetrasporopsidaceae . Tetrasporopsis, Psammochrysis, Chrysomeris.
 * Phaeothamiophyceae
 * Phaeothamniales . Phaeothamnion.
 * Pleurochloridales . Pleurochloridella.
 * Schizocladiophyceae . Schizocladia.
 * Xanthophyceae [Heterokontae ; Heteromonadea  Xanthophyta ]
 * Tribonematales . Botrydium, Bumilleriopsis, Characiopsis, Chloromeson, Heterococcus, Monadus, Ophiocytium, Sphaerosorus, Tribonema, Xanthonema.
 * Vaucheriales . Vaucheria.
 * Diatomista [SIII clade]. Incertae sedis: environmental clades MOCH-1, MOCH-2 and MOCH-4.
 * Bolidophyceae [Parmales ]. Bolidomonas, Triparma, Tetraparma, Pentalamina.
 * Diatomeae [Bacillariophyta ]
 * Leptocylindrophytina
 * Leptocylindrophyceae . Leptocylindrus, Tenuicylindrus.
 * Corethrophyceae . Corethron.
 * Ellerbeckiophytina . Ellerbeckia.
 * Probosciophytina . Proboscia.
 * Melosirophytina . Aulacoseira, Melosira, Hyalodiscus, Stephanopyxis, Paralia, Endictya.
 * Coscinodiscophytina . Actinoptychus, Coscinodiscus, Actinocyclus, Asteromphalus, Aulacodiscus, Stellarima.
 * Rhizosoleniophytina . Guinardia, Rhizosolenia, Pseudosolenia.
 * Arachnoidiscophytina . Arachnoidiscus.
 * Bacillariophytina
 * Mediophyceae
 * Chaetocerotophycidae . Chaetoceros, Bacteriastrum, Dactyliosolen, Cerataulina, Hemiaulus, Eucampia, Acanthoceras, Urosolenia, Terpsinoë, Hydrosera.
 * Lithodesmiophycidae . Lithodesmium, Lithodesmioides, Helicotheca, Bellerochea, Ditylum.
 * Thalassiosirophycidae . Thalassiosira, Lindavia, Cyclotella, Stephanodiscus, Cyclostephanos, Discostella, Bacteriosira, Skeletonema, Detonula.
 * Cymatosirophycidae . Cymatosira, Minutocellus, Papiliocellulus, Leyanella, Extubocellulus, Plagiogrammopsis, Campylosira, Brockmanniella, Pierrecomperia.
 * Odontellophycidae . Odontella, Triceratium, Cerataulus, Pleurosira, Pseudauliscus, Amphitetras, Trieres, Mastodiscus.
 * Chrysanthemodiscophycidae . Chrysanthemodiscus, Biddulphiopsis, Trigonium, Isthmia, Lampriscus, Stictocyclus, Ardissonea, Climacosphenia, Toxarium.
 * Biddulphiophyceae
 * Biddulphiophycidae . Biddulphia.
 * Attheya
 * Bacillariophyceae
 * Striatellaceae . Striatella, Pseudostriatella.
 * Urneidophycidae . (P?) Plagiogramma, Dimeregramma, Rhaphoneis, Delphineis, Psammoneis, Bleakeleya, Asterionellopsis.
 * Fragilariophycidae . Fragilaria, Synedra, Tabellaria, Asterionella, Diatoma, Tabularia, Cyclophora, Astrosyne, Licmophora, Rhabdonema, Grammatophora, Staurosira, Thalassionema.
 * Bacillariophycidae . Eunotia, Achnanthes, Bacillaria, Nitzschia, Pseudonitzschia, Cylindrotheca, Navicula, Seminavis, Haslea, Pleurosigma, Gyrosigma, Achnanthidium, Cocconeis, Frustulia, Diploneis, Sellaphora, Pinnularia, Gomphonema, Cymbella, Didymosphenia, Phaeodactylum, Amphora, Entomoneis, Epithemia, Surirella, etc.
 * Naviculales
 * Stauroneidaceae . Craticula, Dorofeyukea, Fistulifera, Karayevia, Madinithidium, Parlibellus, Prestauroneis, Stauroneis, Schizostauron.
 * Dictyochophyceae [Silicoflagellata ]
 * Dictyochales [Dictyochida ; Dictyochaceae ]. Dictyocha.
 * Florenciellales . Florenciella, Verrucophora.
 * Pedinellales [Ciliophryida ; Actinomonadaceae ]. Actinomonas, Apedinella, Ciliophrys, Mesopedinella, Palatinella, Pedinella, Pseudopedinella, Pteridomonas.
 * Rhizochromulinales [Rhizochromulinaceae ]. Rhizochromulina.
 * Pelagophyceae
 * Pelagomonadales . Aureococcus, Pelagococcus, Pelagomonas.
 * Sarcinochrysidales
 * Sarcinochrysidaceae . Ankylochrisis, Arachnochrysis, Aureoscheda, Aureoumbra, Nematochrysopsis, Pelagospilus, Pulvinaria, Sarcinochrysis, Sargassococcus.
 * Chrysocystaceae . Chrysocystis, Chrysoreinhardia, Sungminbooa.

Alveolata {{au|Cavalier-Smith 1991}}

 * Colponemida (P)
 * Colponemidia . Colponema.
 * Acavomonidia . Acavomonas.
 * Neocolponema
 * Loeffela
 * Palustrimonas

Myzozoa {{au|Cavalier-Smith & Chao 2004}}

 * Colpodellida ["chrompodellids" ; Chromeridophyta  ; Colpodellophyceae ; Chromerida ]. Incertae sedis: Piridium.
 * Vitrellaceae . Vitrella.
 * Colpodellaceae [Colpodellidae ]. Colpodella, Chilovora, Voromonas.
 * Chromeraceae . Chromera.
 * Alphamonaceae . Alphamonas.
 * Perkinsozoa [Perkinsea ]. Incertae sedis genus: Phagodinium,  Rastrimonas.
 * Maranthos
 * Pararosariidae . Pararosarium.
 * Parviluciferaceae . Dinovorax, Parvilucifera, Snorkelia, Tuberlatum.
 * Perkinsidae . Perkinsus.
 * Xcellidae . Cryoxcellia, Gadixcellia, Notoxcellia, Salmoxcellia, Xcellia.
 * Dinoflagellata . Incertae sedis genera: free-living (Adenoides, Akashiwo, Amphidiniella, Ankistrodinium, Apicoporus, Archaeosphaerodiniopsis, Bispinodinium, Bysmatrum, Cabra, Cladopyxis, Crypthecodinium, Cucumeridinium, Dactylodinium, Dicroerisma, Gloeodinium, Grammatodinium, Gynogonadinium, Gyrodiniellum, Halostylodinium, Heterodinium, Moestrupia, Paragymnodinium, Phytodinium, Plagiodinium, Planodinium, Pileidinium, Pseudadenoides, Pseudothecadinium, Pyramidodinium, Rhinodinium, Roscoffia, Sabulodinium, Sphaerodinium, Spiniferodinium, Testudodinium, Thecadinium, Thecadiniopsis, Togula) and parasitic Blastodiniales [no longer valid] (Amyloodinium, Apodinium, Cachonella, Caryotoma, Crepidoodinium, Haplozoon, Oodinium, Myxodinium, Piscinoodinium, Protoodinium, Rhinodinium, Schyzochitriodinium, Stylodinium).
 * Psammosa
 * Oxyrrhis [Oxyrrhinaceae ]
 * Eleftheros
 * Ichthyodinida [environmental Marine Alveolate Group I]
 * Hobagellidae . Hobagella.
 * Euduboscquellidae . Euduboscquella, Dogelodinium, Keppenodinium.
 * Ichthyodiniidae . Ichthyodinium.
 * Syndiniales . Incertae sedis: Ellobiopsidae (Ellobiopsis, Thalassomyces).
 * Amoebophryidae [environmental Marine Alveolate Group II]. Amoebophrya.
 * Syndinidae [environmental Marine Alveolate Group IV]. Hematodinium, Syndinium, Solenodinium.
 * Sphaeriparaceae . Atlanticellodinium, Sphaeripara.
 * Noctilucales [Noctiluciphyceae ]. Abedinium, Cachonodinium, Craspedotella, Cymbodinium, Kofoidinium, Leptodiscus, Noctiluca, Petalodinium, Pomatodinium, Scaphodinium, Spatulodinium.
 * Dinophyceae
 * Gymnodiniphycidae
 * Gymnodiniales sensu stricto. Barrufeta, Chytriodinium, Dissodinium, Erythropsidinium, Greuetodinium, Gymnodinium, Lepidodinium, Nematodinium, Nusuttodinium, Pellucidodinium, Polykrikos, Proterythropsis, Wangodinium, Warnowia.
 * Amphidinium sensu stricto
 * Gyrodinium sensu stricto
 * Kareniaceae . Brachidinium, Karenia, Karlodinium, Takayama.
 * Ceratoperidiniaceae . Ceratoperidinium, Kirithra.
 * Torodiniales . Kapelodinium, Torodinium.
 * Levanderina
 * Margalefidinium
 * Cochlodinium sensu stricto
 * Ptychodiscales . Achradina, Amphilothus, Balechina, Ptychodiscus, Sclerodinium.
 * Borghiellaceae . Baldinia, Borghiella.
 * Tovelliaceae . Bernardinium, Esoptrodinium, Jadwigia, Tovellia.
 * Suessiaceae . Ansanella, Asulcocephalium, Biecheleria, Biecheleriopsis, Leiocephalium, Pelagodinium, Polarella, Prosoaulax, Protodinium, Symbiodinium, Yihiella.
 * Peridiniphycidae
 * Gonyaulacales . Alexandrium, Amylax, Ceratium, Ceratocorys, Coolia, Fukuyoa, Fragilidium, Gambierdiscus, Goniodoma, Gonyaulax, Lingulodinium, Ostreopsis, Pentaplacodinium, Peridiniella, Protoceratium, Pyrocystis, Pyrodinium, Pyrophacus, Tripos.
 * Peridiniales . Amphidiniopsis, Archaeperidinium, Blastodinium*, Diplopelta, Diplopsalis, Diplopsalopsis, Herdmania, Niea, Oblea, Palatinus, Parvodinium, Peridinium, Peridiniopsis, Preperidinium, Protoperidinium, Qia, Vulcanodinium.
 * Thoracosphaeraceae . Aduncodinium, Amyloodinium, Apocalathium, Blastodinium, Chimonodinium, Cryptoperidiniopsis, Duboscquodinium, Ensiculifera, Laciniporus, Leonella, Luciella, Naiadinium, Paulsenella, Pentapharsodinium, Pfiesteria, Scrippsiella, Stoeckeria, Theleodinium, Thoracosphaera, Tintinnophagus, Tyrannodinium.
 * Podolampadaceae . Blepharocysta, Gaarderiella, Heterobractum, Lissodinium, Mysticella, Podolampas.
 * Kryptoperidiniaceae ["dinotoms"]. Blixaea, Durinskia, Galeidinium, Kryptoperidinium, Unruhdinium, etc.
 * Heterocapsaceae . Heterocapsa.
 * Amphidomataceae . Amphidoma, Azadinium.
 * Oxytoxaceae . Corythodinium, Oxytoxum.
 * Centrodiniaceae . Centrodinium.
 * Dinophysales . Amphisolenia, Citharistes, Dinofurcula, Dinophysis, Histioneis, Latifascia, Metadinophysis, Metaphalacroma, Ornithocercus, Oxyphysis, Parahistioneis, Phalacroma, Pseudophalacroma, Sinophysis, Triposolenia.
 * Prorocentrales . Mesoporus, Prorocentrum.
 * Squirmida . Digyalum, Filipodium, Platyproteum.
 * Apicomplexa . Incertae sedis genera: Aggregata, Christalloidophora , Dobellia* , Echinococcidium* , Globidiellum* , Joyeuxella* , Rhabdospora* , Spermatobium* , Spiriopsis* , Spirogregarina* , Toxocystis* , Trophosphaera*.
 * ?Agamococcidiorida . Gemmocystis*, Rhytidocystis.
 * ?Protococcidiorida . Angeiocystis*, Coelotropha*, Grellia*, Eleutheroschizon*, Mackinnonia*, Myriosporides*, Myriospora*, Sawayella*.
 * Aconoidasida [Hematozoa ] (P)
 * Haemospororida . Dionisia*, Haemocystidium, Haemoproteus, Hepatocystis, Leucocytozoon, Mesnilium*, Nycteria, Parahaemoproteus, Plasmodium, Polychromophilus, Rayella*, Saurocytozoon*.
 * Piroplasmorida . Anthemosoma*, Babesia, Cytauxzoon, Echinozoon*, Haemohormidium*, Sauroplasma*, Serpentoplasma*, Theileria.
 * Nephromycida . Nephromyces, Cardiosporidium.
 * Conoidasida (P)
 * Coccidia (P)
 * Adeleorina . Adelea*, Adelina, Babesiosima*, Bartazoon*, Chagasella*, Cyrilia*, Dactylosoma, Desseria*, Ganapatiella*, Gibbsia*, Haemogregarina, Haemolivia, Hepatozoon, Ithania*, Karyolysus, Klossia, Klossiella*, Legerella*, Orcheobius*, Rasajeyna*.
 * Eimeriorina . Atoxoplasma, Barrouxia*, Besnoitia, Caryospora, Caryotropha, Choleoeimeria, Cyclospora, Cystoisospora, Defretinella*, Diaspora*, Dorisa*, Dorisiella*, Eimeria, Elleipsisoma*, Goussia, Hammondia, Hyaloklossia, Isospora, Lankesterella, Mantonella*, Merocystis, Neospora, Nephroisospora, Ovivora*, Pfeifferinella, Pseudoklossia, Sarcocystis, Schellackia, Selenococcidium*, Selysina*, Spirocystis*, Toxoplasma, Tyzzeria*, Wenyonella*.
 * Gregarinasina (P). Incertae sedis genera: Digyalum, Exoschizon.
 * Archigregarinorida (P). Meroselenidium, Merogregarina, Selenidium, Selenocystis, Veloxidium.
 * Eugregarinorida (P). Apolocystis*, Amoebogregarina, Ancora, Ascogregarina, Asterophora, Blabericola, Caliculium, Cephaloidophora, Colepismatophila, Cystobia*, Cystocephalus*, Difficilina, Diplauxis*, Enterocystis, Ganymedes, Geneiorhynchus, Gonospora, Gregarina, Heliospora, Hentschelia*, Hirmocystis*, Hoplorhynchus, Lankesteria, Lecudina, Leidyana, Lithocystis, Monocystella*, Monocystis, Nematopsis, Nematocystis*, Neoasterophora*, Paralecudina, Paraschneideria, Phyllochaetopterus, Pileocephalus*, Polyplicarium, Polyrhabdina, Porospora*, Prismatospora, Protomagalhaensia, Psychodiella, Pterospora, Pyxinia, Pyxinioides, Rhabdocystis*, Sphaerorhynchus*, Steinina, Stenophora, Stylocephalus, Sycia*, Syncystis, Thalicola*, Thiriotia, Trichotokara, Uradiophora*, Urospora, Xiphocephalus, Zygosoma*, and more.
 * Neogregarinorida . Apicystis, Aranciocystis, Caulleryella*, Coelogregarina*, Farinocystis*, Gigaductus*, Lipocystis*, Lipotropha*, Lymphotropha*, Machadoella*, Mattesia, Menzbieria, Ophryocystis, Schizocystis*, Syncystis, Tipulocystis*.
 * Cryptogregarinorida . Cryptosporidium.
 * Blastogregarinea . Chattonaria, Siedleckia.

Ciliophora {{au|Doflein 1901}}

 * Postciliodesmatophora
 * Karyorelictea
 * Kentrophoridae . Kentrophoros.
 * Loxodida
 * Cryptopharyngidae . Cryptopharynx.
 * Loxodidae . Loxodes.
 * Geleiidae . Geleia.
 * Heterotrichea
 * Blepharismidae . Blepharisma
 * Climacostomidae . Climacostomum.
 * Condylostomatidae . Chattonidium, Condylostoma.
 * Fabreidae . Fabrea.
 * Gruberiidae . Gruberia.
 * Coliphorina
 * Folliculinidae . Folliculina.
 * Maristentoridae . Maristentor.
 * Peritromidae . Peritromus.
 * Spirostomidae . Anigsteinia, Spirostomum.
 * Stentoridae . Stentor.
 * Intramacronucleata . Incertae sedis: Protocruziidae [Protocruziidia ] (Protocruzia ).
 * SAL . Incertae sedis: Cariacotrichea (Cariacothrix caudata), Mesodiniidae  (Mesodinium), Phacodiniidia  (Phacodinium).
 * Spirotrichea
 * Euplotia
 * Euplotida
 * Aspidiscidae . Aspidisca.
 * Certesiidae . Certesia.
 * Euplotidae . Euplotes.
 * Gastrocirrhidae . Gastrocirrhus.
 * Uronychidae . Diophrys, Uronychia.
 * Discocephalida
 * Discocephalidae . Discocephalus, Prodiscocephalus, Paradiscocephalus.
 * Pseudoamphisiellidae . Leptoamphisiella, Pseudoamphisiella.
 * Perilemmaphora
 * Hypotrichia
 * Stichotrichida (P)
 * Amphisiellidae . Amphisiella, Bistichella.
 * Atractosidae . Atractos.
 * Epiclintidae . Epiclintes.
 * Gonostomatidae . Cotterillia, Gonostomum.
 * Halteriidae . Halteria, Meseres.
 * Holostichidae . Holosticha, Uncinata.
 * Kahliellidae . Deviata, Kahliella.
 * Keronidae . Kerona.
 * Oxytrichidae (P). Cyrtohymena, Gastrostyla, Oxytricha, Stylonychia.
 * Parabirojimidae . Parabirojimia, Tunicothrix.
 * Plagiotomidae . Plagiotoma.
 * Psammomitridae . Psammomitra.
 * Pseudoamphisiellidae . Pseudoamphisiella.
 * Psilotrichidae . Psilotricha, Urospinula.
 * Schmidingerotrichidae . Schmidingerothrix.
 * Spirofilidae . Spirofilopsis, Strongylidium.
 * Trachelostylidae . Trachelostyla.
 * Uroleptidae . Paruroleptus, Uroleptus.
 * Urostylida (P)
 * Bergeriellidae . Bergeriella, Neourostylopsis.
 * Hemicycliostylidae . Australothrix, Hemicycliostyla.
 * Pseudokeronopsidae . Apoholosticha, Pseudokeronopsis.
 * Pseudourostylidae . Pseudourostyla.
 * Urostylidae . Bakuella, Diaxonella, Urostyla.
 * Oligotrichea
 * Oligotrichida
 * Cyrtostrombidiidae . Cyrtostrombidium.
 * Pelagostrombidiidae . Pelagostrombidium.
 * Strombidiidae . Strombidium (P).
 * Tontoniidae . Laboea, Tontonia.
 * Choreotrichida . Incertae sedis: Lynnella [Lynnellidae ; Lynnellida ]
 * Strobilidiina (P)
 * Leegaardiellidae . Leegaardiella.
 * Lohmanniellidae . Lohmanniella.
 * Strobilidiidae . Strobilidium.
 * Strombidinopsidae . Strombidinopsis (P).
 * Tintinnina . Incertae sedis: Helicostomella, Tintinnopsis (P), several other genera.
 * Ascampbelliellidae . Ascampbelliella
 * Cyttarocylididae [probably synonymous with Petalotrichidae]. Cyttarocylis.
 * Dictyocystidae . Dictyocysta.
 * Epiplocylididae . Epiplocylis.
 * Eutintinnidae . Dartintinnus, Eutintinnus.
 * Favellidae . Favella.
 * Nolaclusiliidae . Nolaclusilis.
 * Petalotrichidae [probably synonymous with Cyttarocylididae]. Petalotricha.
 * Ptychocylididae . Cymatocylis, Ptychocylis.
 * Rhabdonellidae . Metacylis, Rhabdonella, Schmidingerella.
 * Stenosemellidae (P). Stenosemella.
 * Tintinnidae . Amphorellopsis, Salpingacantha, Salpingella, Tintinnus.
 * Tintinnidiidae . Tintinnidium.
 * Undellidae . Undella.
 * Xystonellidae . Dadayiella, Parafavella, Xystonella.
 * Licnophoridae . Licnophora, Prolicnophora.
 * Kiitrichidae . Caryotricha, Kiitricha.
 * Lamellicorticata
 * Armophorea . Incertae sedis: Mylestomatidae (Mylestoma).
 * Metopida (P)
 * Metopidae (P). Bothrostoma, Brachonella, Eometopus, Metopus, Parametopidium, Tesnospira.
 * Apometopidae . Cirranter, Urostomides.
 * Tropidoatractidae . Palmarella, Tropidoatractus.
 * Clevelandellida
 * Clevelandellidae . Clevelandella.
 * Inferostomatidae . Inferostoma.
 * Neonyctotheridae . Neonyctotherus.
 * Nyctotheridae (P). Nyctotherus.
 * Sicuophoridae . Sicuophora.
 * Caenomorphidae . Caenomorpha, Ludio, Sulfonecta.
 * Odontostomatida
 * Discomorphellidae . Discomorphella.
 * Epalxellidae . Epalxella, Saprodinium.
 * Litostomatea
 * Rhynchostomatia
 * Dileptida
 * Dileptidae . Apodileptus, Dileptus, Pseudomonilicaryon.
 * Dimacrocaryonidae . Dimacrocaryon, Monomacrocaryon, Rimaleptus.
 * Tracheliidae . Trachelius.
 * Haptoria (P). Incertae sedis: Chaenea.
 * Lacrymariidae . Lacrymaria.
 * Haptorida
 * Enchelyodonidae . Enchelyodon, Fuscheria.
 * Homalozoonidae . Homalozoon.
 * Pleuroplitidae . Pleuroplites.
 * Didiniidae . Didinium, Monodinium.
 * Pleurostomatida
 * Amphileptidae . Amphileptus.
 * Litonotidae . Litonotus.
 * Kentrophyllidae . Epiphyllum, Kentrophyllum.
 * Spathidiida
 * Acropisthiidae . Acropisthium, Chaenea.
 * Actinobolinidae . Actinobolina.
 * Apertospathulidae . Apertospathula.
 * Enchelyidae . Enchelys.
 * Pseudoholophryidae . Pseudoholophrya.
 * Spathidiidae . Legendrea, Spathidium.
 * Trachelophyllidae . Trachelophyllum.
 * Helicoprorodontidae
 * Trichostomatia
 * Vestibuliferida
 * Balantidiidae . Balantidium, Neobalantidium (P).
 * Buetschliidae . Buetschlia.
 * Paraisotrichidae . Paraisotrichia.
 * Protocaviellidae . Protocaviella.
 * Protohalliidae . Protohallia.
 * Pycnotrichidae . Pycnothrix, perhaps Buxtonella.
 * Isoendo
 * Isotrichidae . Dasytricha, Isotricha.
 * Entodiniomorphida
 * Blepharocorythina
 * Blepharocorythidae . Blepharocorys.
 * Parentodiniidae . Parentodinium.
 * Pseudoentodiniidae . Pseudoentodinium.
 * Entodiniomorphina
 * Cycloposthiidae . Cycloposthium.
 * Gilchristinidae [Gilchristidae ]. Digilchristia, Gilchristina.
 * Ophryoscolecidae . Entodinium, Ophryoscolex, Polyplastron.
 * Polydiniellidae . Polydiniella.
 * Rhinozetidae . Rhinozeta.
 * Spirodiniidae . Spirodinium.
 * Telamodiniidae . Telamodinium.
 * Troglodytellidae . Troglodytella,.
 * Macropodiniida
 * Amylovoracidae . Amylovorax.
 * Macropodiniidae . Macropodinium.
 * Polycostidae . Polycosta.
 * CONTHREEP [Ventrata ]. Incertae sedis: Askenasia, Cyclotrichiidae  (Cyclotrichium), Paraspathidium , Pseudotrachelocercidae  (Pseudotrachelocerca), Discotrichidae  [Discotrichida ] (Discotricha, Lopezoterenia).
 * Phyllopharyngea
 * Synhymeniida
 * Nassulopsidae . Nassulopsis.
 * Orthodonellidae . Orthodonella, Zosterodasys.
 * Scaphidiodontidae . Chilodontopsis, Scaphidiodon.
 * Synhymeniidae . Synhymenia.
 * Subkinetalia
 * Cyrtophoria
 * Chlamydodontida (P)
 * Chilodonellidae . Chilodonella.
 * Chitonellidae . Chitonella.
 * Chlamydodontidae . Chlamydodon.
 * Gastronautidae . Gastronauta.
 * Kryoprorodontidae . Gymnozoum.
 * Lynchellidae . Chlamydonella, Lynchella.
 * Dysteriida
 * Dysteriidae . Dysteria (P), Trochilia.
 * Hartmannulidae (P). Hartmannula.
 * Kyaroikeidae . Kyaroikeus.
 * Plesiotrichopidae . Plesiotrichopus.
 * Chonotrichia
 * Exogemmida
 * Chilodochonidae . Chilodochona.
 * Filichonidae . Filichona.
 * Helichonidae . Heliochona.
 * Lobochonidae . Lobochona.
 * Phyllochonidae . Phyllochona.
 * Spirochonidae . Spirochona.
 * Cryptogemmida
 * Actinichonidae . Actinichona.
 * Echinichonidae . Echinichona.
 * Inversochonidae . Inversochona.
 * Isochonidae . Isochona.
 * Isochonopsidae . Isochonopsis.
 * Stylochonidae . Stylochona.
 * Rhynchodia
 * Hypocomidae . Hypocoma.
 * Rhynchodida
 * Ancistrocomidae . Ancistrocoma.
 * Sphenophryidae . Sphenophrya.
 * Suctoria
 * Exogenida
 * Allantosomatidae . Allantosoma.
 * Dentacinetidae . Dentacineta.
 * Dendrosomididae . Dendrosomides.
 * Ephelotidae . Ephelota.
 * Lecanophryidae . Lecanophrya.
 * Manuelophryidae . Manuelophrya.
 * Metacinetidae . Metacineta.
 * Ophryodendridae . Ophryodendron.
 * Paracinetidae . Paracineta.
 * Phalacrocleptidae . Phalacrocleptes.
 * Podophryidae . Podophrya.
 * Praethecacinetidae . Praethecacineta.
 * Rhabdophryidae . Rhabdophrya.
 * Severonidae . Severonis.
 * Spelaeophryidae . Spelaeophrya.
 * Tachyblastonidae . Tachyblaston.
 * Thecacinetidae . Thecacineta.
 * Endogenida
 * Acinetidae . Acineta.
 * Acinetopsidae . Acinetopsis.
 * Choanophryidae . Choanophrya.
 * Corynophryidae . Corynophrya.
 * Dactylostomatidae . Dactylostoma.
 * Dendrosomatidae . Dendrosoma.
 * Endosphaeridae . Endosphaera.
 * Erastophryidae . Erastophrya.
 * Pseudogemmidae . Pseudogemma.
 * Rhynchetidae . Rhyncheta.
 * Solenophryidae . Solenophrya.
 * Tokophryidae . Tokophrya.
 * Trichophryidae . Trichophrya.
 * Evaginogenida
 * Cometodendridae . Cometodendron.
 * Cyathodiniidae . Cyathodinium.
 * Dendrocometidae . Dendrocometes.
 * Discophryidae . Discophrya.
 * Enchelyomorphidae . Enchelyomorpha.
 * Heliophryidae . Heliophrya.
 * Periacinetidae . Periacineta.
 * Prodiscophryidae . Prodiscophrya.
 * Rhynchophryidae . Rhynchophrya.
 * Stylocometidae . Stylocometes.
 * Trypanococcidae . Trypanococcus.
 * Colpodea
 * Bursariomorphida
 * Bryometopidae . Bryometopus (P), Thylakidium.
 * Bursaridiidae . Bursaridium, Paracondylostoma.
 * Bursariidae . Bursaria.
 * Colpodida . Incertae sedis: Bardeliellidae (Bardeliella), Hausmanniellidae  (Avestina, Hausmanniella), Ilsiellidae  (Ilsiella), Pseudochlamydonellidae  (Hackenbergia, Pseudochlamydonella) and Marynidae  (Maryna).
 * Bryophryina
 * Bryophryidae . Bryophrya.
 * Sandmanniellidae . Sandmanniella.
 * Colpodina
 * Colpodidae (P). Colpoda.
 * Grandoriidae . Grandoria.
 * Tillinidae . Tillina.
 * Grossglockneriidae [Grossglockneriina ]. Grossglockneria, Pseudoplatyophrya.
 * Cyrtolophosidida
 * Cyrtolophosididae . Cyrtolophosis.
 * Kreyellidae . Kreyella.
 * Platyophryida
 * Ottowphryidae . Ottowphrya, Platyophryides.
 * Platyophryidae (P). Platyophrya.
 * Sagittariidae . Sagittaria.
 * Sorogenidae . Sorogena.
 * Woodruffiidae . Etoschophrya, Rostrophrya, Woodruffia.
 * Nassophorea (P)
 * Colpodidiidae . Colpodidium.
 * Nassulida
 * Furgasoniidae . Furgasonia, Wolfkosia.
 * Nassulidae . Nassula, Obertrumia.
 * Microthoracida
 * Microthoracidae . Drepanomonas, Microthorax.
 * Leptopharyngidae . Leptopharynx, Pseudomicrothorax.
 * Prostomatea (P)
 * Apsiktratidae [Prostomatida ]
 * Balanionidae . Balanion.
 * Cryptocaryonidae . Cryptocaryon.
 * Colepidae . Coleps, Plagiopogon.
 * Holophryidae . Holophrya.
 * Lagynidae . Lagynus.
 * Metacystidae . Metacystis, Vasicola.
 * Placidae . Placus.
 * Plagiocampidae . Plagiocampa.
 * Prorodontidae . Prorodon.
 * Urotrichidae . Urotricha.
 * Plagiopylea
 * Plagiopylida
 * Epalxellidae . Epalxella, Saprodinium.
 * Plagiopylidae . Plagiopyla.
 * Sonderiidae . Sonderia.
 * Trimyemidae . Trimyema.
 * Oligohymenophorea
 * Apostomatia
 * Apostomatida
 * Colliniidae . Collinia, Metacollinia.
 * Cyrtocaryidae . Cyrtocaryum.
 * Foettingeriidae . Foettingeria.
 * Pseudocolliniidae . Fusiforma, Pseudocollinia.
 * Astomatophorida
 * Opalinopsidae . Opalinopsis.
 * Pilisuctorida
 * Conidophryidae . Conidophrys.
 * Astomatia
 * Anoplophryidae . Anoplophrya.
 * Buetschliellidae . Buetschliella.
 * Clausilocolidae . Clausilocola.
 * Contophryidae . Contophyra.
 * Haptophryidae . Haptophrya.
 * Hoplitophryidae . Hoplitophrya.
 * Intoshellinidae . Intoshellina.
 * Maupasellidae . Maupasella.
 * Radiophryidae . Radiophrya.
 * Hymenostomatia
 * Tetrahymenida . Incertae sedis: Trichospiridae (Trichospira).
 * Curimostomatidae . Curimostoma.
 * Glaucomidae . Glaucoma.
 * Spirozonidae . Spirozona.
 * Tetrahymenidae . Tetrahymena.
 * Turaniellidae . Colpidium, Dexiostoma, Turaniella.
 * Ophryoglenida
 * Ichthyophthiriidae . Ichthyophthirius.
 * Ophryoglenidae . Ophryoglena.
 * Peniculia (P)
 * Peniculida
 * Clathrostomatidae . Clathrostoma.
 * Frontoniidae . Disematostoma, Frontonia (P).
 * Lembadionidae . Lembadion.
 * Maritujidae . Marituja.
 * Neobursaridiidae . Neobursaridium.
 * Parameciidae . Paramecium.
 * Paranassulidae . Paranassula.
 * Stokesiidae . Stokesia.
 * Urocentridae [Urocentrida ]
 * Peritrichia
 * Sessilida
 * Astylozoidae . Astylozoon, Hastatella.
 * Ellobiophryidae . Ellobiophrya.
 * Epistylididae . Epistylis.
 * Lagenophryidae . Lagenophrys.
 * Operculariidae . Opercularia.
 * Rovinjellidae . Rovinjella.
 * Scyphidiidae (P). Scyphidia.
 * Termitophryidae . Termitophrya.
 * Usconophryidae . Usconophrys.
 * Vaginicolidae . Cothurnia, Pyxicola, Thuricola, Vaginicola.
 * Vorticellidae . Carchesium, Epicarchesium (P), Ophrydium, Pelagovorticella, Pseudovorticella (P), Vorticella (P).
 * Zoothamniidae . Haplocaulus, Zoothamnium.
 * Mobilida
 * Polycyclidae . Polycycla.
 * Trichodinidae . Trichodina.
 * Trichodinopsidae . Trichodinopsis.
 * Urceolariidae . Leiotrocha, Urceolaria.
 * Scuticociliatia (P)
 * Philasterida
 * Cohnilembidae . Cohnilembus.
 * Cryptochilidae . Cryptochilum.
 * Entodiscidae . Entodiscus.
 * Entorhipidiidae . Entorhipidium.
 * Orchitophryidae (P). Orchitophrya.
 * Paralembidae . Anophrys, Paralembus.
 * Parauronematidae (P). Parauronema (P).
 * Philasteridae . Kahlilembus, Philaster.
 * Pseudocohnilembidae . Pseudocohnilembus.
 * Schizocaryidae . Schizocaryum.
 * Thigmophryidae . Thigmophrya.
 * Thyrophylacidae . Thyrophylax.
 * Uronematidae . Uronema.
 * Urozonidae . Urozona.
 * Pleuronematida
 * Calyptotrichidae . Calyptotricha.
 * Conchophthiridae . Conchophthirus.
 * Ctedoctematidae . Ctedoctema.
 * Cyclidiidae (P). Cristigera, Cyclidium.
 * Dragescoidae . Dragescoa.
 * Eurystomatellidae . Eurystomatella.
 * Histiobalantiidae . Histiobalantium.
 * Peniculistomatidae . Peniculistoma.
 * Pleuronematidae (P). Pleuronema.
 * Thigmocomidae . Thigmocoma.
 * Thigmotrichida
 * Ancistridae . Ancistrum.
 * Hemispeiridae . Hemispeira.
 * Hysterocinetidae . Hysterocineta.
 * Paraptychostomidae . Paraptychostomum.
 * Loxocephalida (P)
 * Cinetochilidae (P). Cinetochilum, Sathrophilus.
 * Loxocephalidae . Cardiostomatella, Dexiotricha, Loxocephalus.

Rhizaria {{au|Cavalier-Smith 2002}}
Rhizaria incertae sedis: Gymnosphaerida. Actinocoryne, Cienkowskya, Gymnosphaera, Hedraiophrys [possible synonym of Cienkowskya], Wagnerella.

Cercozoa {{au|Cavalier-Smith 1998, emend. Adl et al. 2005; emend. Cavalier-Smith 2018}}

 * Cercozoa incertae sedis:
 * Aquavolonida . Aquavolon, Lapot.
 * Tremulida . Tremula.
 * Genera of uncertain placement: Dictiomyxa, Katabia, Myxodictyium, Pontomyxa, Protomyxa, Protogenes, Pseudospora, Rhizoplasma
 * Discocelia [Discocelis ]
 * Psammonobiotidae* . Alepiella, Chardezia, Edaphonobiotus, Feuerbornia, Frenzelina, Lesquerella, Micramphora, Micropsammella, Nadinella, Ogdeniella, Psammonobiotus, Propsammonobiotus, Rhumbleriella.
 * Sarcomonadea (P)
 * Cercomonadida [Cercomonadidae ; Cercobodonidae ]. Cercomonas, Eoercomonas, Filomonas, Neocercomonas, Cavernomonas.
 * Paracercomonadida [Paracercomonadidae ]. Brevimastigomonas, Metabolomonas, Nucleocercomonas, Paracercomonas, Phytocercomonas.
 * Glissomonadida [Heteromitidae ]
 * Saccharomycomorphidae . Saccharomycomorpha.
 * Sandonidae . Sandona, Flectomonas, Neoheteromita, Mollimonas.
 * Dujardinidae . Dujardina.
 * Bodomorphidae . Bodomorpha.
 * Proleptomonadidae . Proleptomonas.
 * Allapsidae . Allapsa, Teretomonas, Allantion.
 * Viridiraptoridae . Orciraptor, Viridiraptor.
 * Pansomonadidae . Agitata, Aurigamonas.
 * Sainouroidea [Helkesida ]
 * Sainouridae . Acantholus, Cholamonas, Homocognata, Sainouron.
 * Helkesimastigidae . Helkesimastix.
 * Guttulinopsidae . Guttulinopsis, Olivorum, Puppisaman, Rosculus.
 * Thecofilosea . Incertae sedis: Mataza.
 * Phaeodarea [Tripylea ]
 * Phaeoconchia . Coelodendrum, Coelographis, Conchellium, Conchopsis.
 * Phaeocystina . Aulacantha, Aulographis, Cannoraphis.
 * Phaeogromia . Castanella, Challengeron, Haeckeliana, Medusetta, Tuscarora.
 * Phaeosphaeria . Aulosphaera, Cannosphaera, Sagosphaera.
 * Cryomonadida
 * Rhogostomidae . Rhogostoma, Sacciforma, Capsellina.
 * Protaspidae [Cryomonadidae ]. Cryothecomonas, Protaspa.
 * Ventricleftida
 * Ventrifissuridae . Ventrifissura.
 * Verrucomonadidae . Verrucomonas.
 * Tectofilosida
 * Chlamydophryidae . Chlamydophryse, Diaphoropodon, Lecythium, Trachyrhizium.
 * Psammonobiotidae . Micropsamella.
 * ?Volutellidae . Pseudovolutella, Volutella.
 * Fiscullina
 * Fiscullidae . Fisculla, Omnivora.
 * Pseudodifflugiidae . Pseudodifflugia.
 * Rhizaspididae . Rhizaspis.
 * Ebriacea [Ebriidae ; Ebriida ]. Ebria, Hermesinum, Botuliforma.
 * Imbricatea
 * Spongomonadida [Spongomonadidae ]. Rhipidodendron, Spongomonas.
 * Marimonadida
 * Abolliferidae . Abollifer, Cowlomonas, ?Heterochromonas.
 * Auranticordidae . Auranticordis, Rhabdamoeba.
 * Cyranomonadidae . Cyranomonas.
 * Pseudopirsoniidae . Pseudopirsonia.
 * Variglissida
 * Clautriaviidae . Clautriavia.
 * Nudifilidae . Nudifila.
 * Quadriciliidae . Quadricilia.
 * Silicofilosea
 * Thaumatomonadida [Thaumatomastigidae ]
 * Thaumatomonadidae . Allas, Hyaloselene, Reckertia, Thaumatomonas, Thaumatomastix, Ovaloplaca, Scutellomonas, Thaumatospina, Penardeugenia.
 * Peregriniidae . Gyromitus, Peregrinia.
 * Esquamulidae . Esquamula.
 * Euglyphida . Incertae sedis: Phaeobola.
 * Cyphoderiidae . Campascus*, Corythionella, Cyphoderia [Schaudinnula], Messemvriella*, Pseudocorythion, Ichthyosquama, Knarr, Oleiformis, Psammoderia.
 * Paulinellidae . Micropyxidiella, Ovulinata, Paulinella.
 * Euglyphina
 * Assulinidae . Assulina, Placocista, Valkanovia*.
 * Sphenoderiidae . Sphenoderia, Trachelocorythion, Deharvengia*.
 * Trinematidae . Corythion, Playfairina*, Puytoracia*, Trinema.
 * Euglyphidae . Euglypha, Scutiglypha.
 * Tracheleuglypha
 * Trivalvulariida . Leptogromia, Trivalvularis.
 * Metromonadea . Metromonas, Metopion, Micrometopion, Kiitoksia.
 * Granofilosea . Incertae sedis granofilosean genera*: ?Apogromia, ?Kibisidytes, ?Leucodictyon, ?Limnofila, ?Mesofila, ?Microcometes, ?Microgromia, ?Nanofila, ?Reticulamoeba and probably ?Belaria, ?Ditrema, ?Heliomorpha [=Dimorpha] and ?Paralieberkuehnia.
 * Massisteridae . Massisteria, Minimassisteria.
 * Clathrulinidae [Desmothoracida ]. Actinosphaeridium, Cienkowskya*, Clathrulina, Hedriocystis, Penardiophrys, ?Servetia.
 * Chlorarachnea . Amorphochlora, Bigelowiella, Chlorarachnion, Cryptochlora, Gymnochlora, Lotharella, Minorisa, Partenskyella, Viridiuvalis.

Endomyxa {{au|Cavalier-Smith 2002, emend. Bass & Berney in Adl et al. 2019}}

 * Vampyrellida [Aconchulinida ]. Incertae sedis: Arachnula, Gobiella, Lateromyxa, Penardia.
 * Thalassomyxa
 * Vampyrellidae . Vampyrella.
 * Leptophryidae . Arachnomyxa, Leptophrys, Planctomyxa, Platyreta, Pseudovampyrella, Theratromyxa, Vernalophrys.
 * Placopodidae [Hyalodiscidae ]. Placopus.
 * Sericomyxidae . Sericomyxa.
 * Phytomyxea
 * Marinomyxa
 * Plasmodiophorida [Plasmodiophorales ; Plasmodiophoromycota  ]. Plasmodiophora [Ostenfeldiella], Polymyxa, Woronina, Ligniera [Anisomyxa; Rhizomyxa; Sorolpidium], Sorosphaerula [Tuburcinia; Sorosporium], Spongospora [Clathrosorus], ?Membranosorus, ?Octomyxa, ?Polymyxa, ?Sorodiscus, ?Tetramyxa [Molliardia; Thecaphora].
 * Phagomyxida . Phagomyxa, Maullinia.
 * Filoreta
 * Gromia
 * Ascetosporea
 * Haplosporida . Bonamia, Haplosporidium, Minchinia, Urosporidium.
 * Mikrocytida . Mikrocytos, Paramikrocytos.
 * Paramyxida . Marteilia, Paramyxa, Paramarteilia, Marteilioides, Eomarteilia.
 * Claustrosporidium
 * Paradiniida . Paradinium.

Retaria {{au|Cavalier-Smith 2002}}

 * Foraminifera . Incertae sedis groups: ?Lagenida, ?Heterogromia, ?Komokiacea*.
 * Monothalamids (P) [currently under revision]. All genera traditionally in Allogromiida, Astrorhizida, and the Xenophyophorea. Genera unplaced into families: Allogromia, Astrammina, Crithionina, Notodendrodes, Psammophaga, Bathysiphon.
 * Nujappikia
 * Allogromiidae . Vellaria.
 * Lieberkuehniidae . Lieberkuehnia, Claparedellus.
 * Edaphoallogromiidae . Edaphoallogromia.
 * Lacogromiidae . Lacogromia.
 * Limnogromiidae . Limnogromia.
 * Reticulomyxidae . Reticulomyxa, Dracomyxa, Haplomyxa, Wobo.
 * Schizamminidae . Jullienella, Schizammina, Spiculosiphon.
 * Velamentofexidae . Velamentofex.
 * Tubothalamea . Fusulinida probably belongs to this group.
 * Miliolida . Alveolina, Cornuspira, Miliammina, Pyrgo, Quinqueloculina, Sorites.
 * Spirillinida . Patellina, Spirillina.
 * Ammodiscidae . Ammodiscus, Glomospira.
 * Globothalamea
 * Rotaliida
 * Planorbulinidae . Planorbulinella, Hyalinea.
 * Discorboidea
 * Discorbidae . Discorbis.
 * Rosalinidae . Rupertina, Discanomalina, "Rosalina", Gavelinopsis, Planorbulina.
 * Rotalioidea . Incertae sedis genera: ?Criboelphidium, ?"Elphidium", ?Protelphidium.
 * Elphidiidae . Elphidium.
 * Ammoniidae . Ammonia.
 * Elphidiellidae . Elphidiella.
 * Haynesinidae . Haynesina, Aubignyna.
 * Glabratelloidea
 * Rotaliellidae . Rotaliella, Rossyatella.
 * Buliminoididae . Buliminoides.
 * Glabratellidae . Glabratella, Glabratellina, Angulodiscorbis, Planoglabratella.
 * Calcarinoidea
 * Calcarinidae . Neorotalia, Baculogypsina, Baculogypsinoides, Schlumbergerella, Pararotalia.
 * Nummulitoidea
 * Nummulitidae . Nummulites, Operculinella, Cycloclypeus, Heterostegina, Operculina, Planoperculina, Planostegina.
 * Serioidea
 * Uvigerinidae . Uvigerina, Rectuvigerina, Trifarina.
 * Bolivinitidae . Bolivina, Brizalina, Saidovina.
 * Cassidulinidae . Globocassidulina, Cassidulinoides, Evolvocassidulina, Islandiella, Ehrenbergina
 * Sphaeroidinidae . Sphaeroidina.
 * Globobuliminidae . Globobulimina.
 * Incertae sedis Rotaliida families:
 * ?Nonionidae . Nonion, Nonionella, Nonionellina, Nonionoides.
 * ?Virgulinellidae . Virgulinella.
 * ?Buliminidae . Bulimina.
 * ?Epistominellidae . Epistominella.
 * ?Stainforthiidae . Stainforthia, Gallitellia.
 * ?Cibicididae . Cibicides, Cibicidoides, Heterolepa.
 * ?Chilostomellidae . Chilostomella.
 * ?Pullenidae . Pullenia.
 * ?Nuttalidae . Nuttalides.
 * ?Discorbinellidae . Discorbinella, Hanzawaia.
 * ?Astrononionidae . Astrononion.
 * ?Oridorsalidae . Oridorsalis.
 * ?Melonidae . Melonis.
 * ?Cymbaloporidae . Cymbaloporella.
 * ?Rubratelliidae . Rubratella.
 * ?Murrayinelliidae . Murrayinella.
 * Globigerinida (P)
 * Parvularugoglobigerinoidea
 * Parvularuglobigerinidae . Pseudocaucasina, Palaeoglobigerina, Parvularugoglobigerina.
 * Eoglobigerinoidea
 * Eoglobigerinidae . Alicantina, Eoclavatorella, Eoglobigerina, Parasubbotina, Pseudoglobigerinella, Subbotina, Turbeogloborotalia.
 * Globoquadrinidae . Dentoglobigerina, Globoquadrina.
 * Neoacarininidae . Neoacarinina.
 * Porticulasphaeridae . Globigerinatheka, Guembelitrioides, Inordinatosphaera, Orbulinoides, Porticulasphaera.
 * Globigerinoidea
 * Globigerinidae . Alloglobigerinoides, Ciperoella, Globigerina, Globicuniculus, Globigerinoides, Globigerinoidesella, Globoturborotalita, Trilobigerina [Trilobatus], Zeaglobigerina.
 * Globigerinellidae . Beella, Bolliella, Globigerinella, Orcadia, Protentella, Quiltyella.
 * Hastigerinidae . Hastigerina, Hastigerinella, Hastigerinopsis.
 * Orbulinidae . Biorbulina, Candorbulina, Orbulina, Praeorbulina.
 * Sphaeroidinellidae . Prosphaeroidinella, Sphaeroidinella, Sphaeroidinellopsis.
 * Turborotalitidae . Berggrenia, Turborotalita.
 * Globorotalioidea
 * Catapsydracidae . Catapsydrax, Globigerinopsoides, Globigerinoita, Velapertina.
 * Globorotaloididae . Clavatorella, Globorotaloides, Protentelloides.
 * Globorotaliidae . Dentigloborotalia, Globoconella, Globorotalia, Hirsutella, Jenkinsella, Menardella, Neogloboquadrina, Paragloborotalia, Truncorotalia.
 * Pulleniatinidae . Pulleniatina.
 * Globanomalinidoidea
 * Globanomalinidae . Carinoturborotalia, Globanomalina, Luterbacheria, Planoglobanomalina, Turborotalia.
 * Hantkeninoidea
 * Pseudohastigerinidae . Pseudohastigerina.
 * Hantkeninidae . Applinella, Aragonella, Clavigerinella, Cribrohantkenina, Hantkenina.
 * Truncorotaloidinoidea
 * Globigerapsidae . Globigerapsis, Muricoglobigerina.
 * Planorotalitidae . Astrorotalia, Planorotalites.
 * Truncorotaloididae . Acarinina, Igorina, Morozovella, Morozovelloides, Pearsonites, Praemurica, Pseudogloboquadrina, Testacarinata, Truncorotaloides.
 * Globotruncanida
 * Abathomphaloidea
 * Abathomphalidae . Abathomphalus.
 * Globotruncanellidae . Globotruncanella, Spinoglobotruncanella.
 * Favuselloidea
 * Conoglobigerinidae . Conoglobigerina, Tenuigerina, ?Sphaerogerina.
 * Favusellidae . Ascoliella, Favusella, Koutsoukosia.
 * Globuligerinidae . Compactogerina, Globuligerina, Haeuslerina, Petaloglobigerina.
 * Hedbergelloidea
 * Ananiidae . Anania, Badriella, Costellagerina, Hillsella, Liuenella [Liuella], Loeblichella, Muricohedbergella, Paracostellagerina, Pessagnoina, Planohedbergella, Pseudoclavihedbergella, Vanhintella.
 * Hedbergellidae . Asterohedbergella, Clavihedbergella, Hedbergella, Microhedbergella, Paraticinella, Pseudoguembelitria.
 * Helvetoglobotruncanidae . Angulocarinella, Bermudeziana, Bollitruncana, Fingeria, Hedbergellita, Brittonella, Helvetoglobotruncana, Unitruncatus, Whiteinella.
 * Praehedbergellidae . Blefuscuiana, Gorbachikella, Praehedbergella, Lilliputianella, Lilliputianelloides, Wondersella.
 * Globotruncanoidea
 * Globotruncanidae . Contusotruncana, Globotruncana, Marginotruncana, Obliquacarinata, Sphaerotruncana, Ventrotruncana.
 * Praeglobotruncanidae . Concavatotruncana, Dicarinella, Falsotruncana, Rotundina, Praeglobotruncana, Verotruncana.
 * Reissidae . Elevatotruncana, Globotruncanita, Kassabiana, Radotruncana, Sigalitruncana, Turbotruncana.
 * Planomalinoidea
 * Eohastigerinellidae . Eohastigerinella, Hastigerinoides.
 * Globigerinelloididae . Alanlordella, Allotheca, Biglobigerinella, Blowiella, Claviblowiella, Globigerinelloides, Pseudoschackoina.
 * Planomalinidae . Bannerina, Planomalina, Pseudoplanomalina.
 * Schackoinidae . Asymetria, Groshenyia, Leupoldina, Neoschackoina, Schackoina.
 * Rotaliporoidea
 * Rotaliporidae . Anaticinella, Pseudothalmanninella, Rotalipora, Thalmanninella.
 * Ticinellidae . Biticinella, Claviticinella, Ticinella.
 * Rugoglobigerinoidea
 * Helvetiellidae . Archaeoglobigerina, Bucherina, Dorbignya, Edgarinella, Gandolfia, Gansserina, Globocarinata, Helvetiella, Kuglerina.
 * Rugoglobigerinidae . Archaeoglobitruncana, Plummerita, Rugoglobigerina, Rugosocarinata, Rugotruncana, Trinitella.
 * Heterohelicida
 * Heterohelicoidea
 * Gublerinidae . Gublerina, Lipsonia, Praegublerina.
 * Heterohelicidae . Braunella, Bronnimannella, Ehrenbergites, Globoheterohelix, Fleisherites, Hartella, Heterohelix, Huberella, Laeviheterohelix, Lazarusina, Lunatriella, Magellanina, Mihaia, Nederbragtina, Planoheterohelix, Protoheterohelix, Pseudoplanoglobulina, Steineckia, Striataella, Texasina, ?Bifarina, ?Rectoguembelina, ?Zeauvigerina.
 * Pseudotextulariidae . Planoglobulina, Pseudotextularia, Racemiguembelina.
 * Pseudoguembelinidae . Eicheriella, Leptobimodalia, Pseudoguembelina.
 * Spiroplectidae . Hendersonites [Hendersonia], Neohendersonites, Paraspiroplecta, Spiroplecta.
 * Ventilabrellidae . Planulitella, Proliferania, Sigalia, Ventilabrella.
 * Guembelitriida
 * Cassigerinelloidea
 * Cassigerinellidae . Cassigerinella, Riveroinella.
 * Guembelitrioidea
 * Guembelitriidae . Cassigerinelloita, Guembelitria, Chiloguembelitria, Jenkinsina, ?Archaeoguembelitria, ?Gallitellia, ?Guembelitriella.
 * Chiloguembelinoidea
 * Chiloguembelinidae . Chiloguembelina, Woodringina, ?Streptochilus.
 * Globoconusoidea
 * Globoconusidae . Globoconusa, Trochoguembelitria,
 * Order ? (unnamed)
 * Globigerinitoidea
 * Candeinidae . Candeina.
 * Globigerinatellidae . Globigerinatella.
 * Globigerinitidae . Globigerinita, Mutabella, Polyperibola, Tinophodella.
 * Tenuitellidae . Praetenuitella, Tenuitella, Tenuitellinata, Tenuitellita.
 * Family ? (unnamed). Dipsidripella, ?Antarcticella.
 * Robertinida . Hoeglundina, Robertina, Robertinoides.
 * Textulariida (P). Cyclammina, Eggerella, Reophax, Textularia, Trochammina.
 * Carterinida . Carterina.
 * Radiolaria
 * Acantharea
 * Chaunocanthida . Amphiacon, Conacon, Gigartacon, Heteracon, Stauracon.
 * Holocanthida . Acanthochiasma, Acanthocolla, Acanthoplegma.
 * Symphyacanthida . Amphilithium, Astrolonche, Pseudolithium.
 * Arthracanthida . Acanthometra, Daurataspis, Dictyacantha, Diploconus, Phractopelta, Phyllostaurus, Pleuraspis, Stauracantha.
 * Taxopodida . Sticholonche.
 * Polycystinea
 * Spumellaria . Actinomma, Didymocyrtis, Euchitonia, Hexacontium, Hexalonche, Hexastylus, Octodendron, Plegmosphaera, Saturnalis, Spongaster, Spongosphaera.
 * Nassellaria . Artostrobus, Eucyrtidium, Lithomelissa, Pterocanium, Pterocorys.
 * Collodaria . Acrosphaera, Collosphaera, Collozoum, Sphaerozoum, Rhaphidozoum, Siphonsphaera, Thalassicolla.
 * Orodaria
 * Oroscenidae [Orosphaerida ; Orosphaeridae ]. Oroscena, Orostaurus, Oropelex. Nomina dubia genera: Orosphaera, Orodictyum, Orona, Oronium.
 * Thalassothamnidae [Cytocladidae ]. Thalassothamnus, Cytocladus. Nomen dubium genus: Conostylus.
 * Entactinaria
 * Entactiniidae . Afanasievella, Apophysiactinia, Borisella, Callela, Cancellosphaera, Costaentactinia, Cyclocarpus, Duodecimentactinia, Langsonsphaera, Entactinosphaera, Gracilentactinia, Holdisphaera, Involutentactinia, Kashiwara, Magnentactinia, Magnisphaera, Microporosa, Moskovistella, Multientactinia, Munzuwonella, Paratriposphaera, Perforentactinia, Plenoentactinia, Plenosphaera, Pluristratoentactinia, Polyedroentactinia, Provisocyntra, Radiobisphaera, Retentactinia, Retisphaera, Sinosphaera, Spongentactinia, Stigmosphaerostylus, Trilonche, Uberinterna, Wuyia.
 * Tetrentactiniidae . Multisphaera.
 * Triassothamnidae . Triassothamnus.

Haptista {{au|Cavalier-Smith 2003}}

 * Haptophyta
 * Pavlovales [Pavlovophyceae ]. Diacronema, Exanthemachrysis, Pavlova, Rebecca.
 * Prymnesiophyceae
 * Prymnesiales . Chrysochromulina, Chrysocampanula, Dicrateria, Haptolina, Prymnesium, Pseudohaptolina.
 * Phaeocystales . Phaeocystis.
 * Isochrysidales . Emiliania, Gephyrocapsa, Isochrysis, Ruttnera, Tisochrysis.
 * Coccolithales . Balaniger, Calciosolenia, Coccolithus, Hymenomonas, Chrysotila, Wigwamma.
 * Rappephyceae
 * Pavlomulinales . Pavlomulina.
 * Centroplasthelida [Centrohelea ; Centroheliozoa ]
 * ?Parasphaerastrum.
 * ?Spiculophryidae . Spiculophrys.
 * Pterocystida
 * Raphidista
 * Choanocystidae . Choanocystis.
 * Raphidiophryidae . Raphidiophrys.
 * Pterista
 * Oxnerellidae . Oxnerella.
 * Pterocystidae . Pterocystis, Raineriophrys, Chlamydaster, Pseudoraphidiophrys, Pseudoraphidocystis, Triangulopteris.
 * Heterophryidae . Heterophrys, Sphaerastrum.
 * Panacanthocystida
 * Yogsothothidae [Chthonida ; Yogsothothina ]. Yogsothoth.
 * Acanthocystida
 * Marophryidae [Marophryina ]. Marophrys.
 * Chalarothoracina
 * Acanthocystidae . Acanthocystis.
 * Raphidocystidae . Raphidocystis.

Cryptista {{au|Cavalier-Smith 1989, 2018, emend. Adl et al. 2019}}

 * Palpitomonas bilix
 * Cryptophyceae [Cryptophyta ; Cryptophyta ]
 * ?Bjornbergiella
 * Cryptomonadales . Chroomonas, Cryptomonas, Falcomonas, Geminigera, Guillardia, Hanusia, Hemiselmis, Plagioselmis, Proteomonas, Rhinomonas, Rhodomonas, Storeatula, Teleaulax.
 * Cyathomonadacea . Goniomonas [previously Cyathomonas], Hemiarma.
 * Kathablepharididae [Kathablepharidaceae ; Leucocryptea ]. Hatena, Kathablepharis, Leucocryptos, Platychilomonas, Roombia.

Incertae sedis Eukarya

 * Meteora sporadica Hausmann, Weitere, Wolf & Arndt, 2002

Hemimastigophora {{au|Foissner et al. 1988}}

 * Spironematellidae [Spironemidae ]. Hemimastix, Spironematella [Spironema ], Stereonema.
 * Paramastigidae . Paramastix.

Malawimonadida {{au|Cavalier-Smith 2003}}

 * Malawimonadidae . Gefionella, Malawimonas.
 * Imasidae . Imasa.

Metamonada {{au|Grassé 1952, emend. Cavalier-Smith 1987}}

 * ?Barthelona
 * Anaeramoebae [Anaeramoebidae ]. Anaeramoeba.
 * Fornicata
 * "Carpediemonas-like organisms" (P). Aduncisulcus, Carpediemonas, Dysnectes, Ergobibamus, Hicanonectes, Kipferlia.
 * Diplomonadida
 * Hexamitinae . Enteromonas, Gyromonas*, Hexamita, Spironucleus, Trepomonas, Trigonomonas*, Trimitus.
 * Giardiinae . Brugerolleia*, Giardia, Octomitus.
 * Retortamonadida (P). Chilomastix, Retortamonas.
 * Caviomonadidae . Caviomonas*, Iotanema.
 * Parabasalia
 * ?Tricercomitus
 * Trichomonadida . Cochlosoma, Dientamoeba, Lacusteria, Pentatrichomonas, Pentatrichomonoides, Pseudotrichomonas, Pseudotrypanosoma, Tetratrichomonas, Trichomonas, Trichomonoides, Trichomitopsis.
 * Honigbergiellida (P?). Ditrichomonas, Cthulhu, Cthylla, Hexamastix, Honigbergiella, Monotrichomonas.
 * Hypotrichomonadida . Hypotrichomonas, Trichomitus.
 * Tritrichomonadida (P?). Dientamoeba, Histomonas, Monocercomonas, Parahistomonas, Simplicimonas, Tritrichomonas.
 * Cristamonadida . Caduceia, Calonympha, Coronympha, Deltotrichonympha, Devescovina, Foaina, Gigantomonas, Joenia, Joenina, Joenoides, Joenopsis*, Kofoidia, Koruga, Macrotrichomonas, Macrotrichomonoides, Metadevescovina, Mixotricha, Pachyjoenia*, Projoenia*, Pseudodevescovina, Rhizonympha*, Snyderella, Stephanonympha.
 * Spirotrichonymphida . Holomastigotes*, Holomastigotoides, Microjoenia*, Micromastigotes*, Rostronympha*, Spiromastigotes*, Spironympha*, Spirotrichonympha*, Spirotrichonymphella, Uteronympha*.
 * Lophomonadida . Lophomonas.
 * Trichonymphida . Barbulanympha, Eucomonympha, Heliconympha, Hoplonympha, Leptospironympha, Macrospironympha*, Pseudotrichonympha, Rhynchonympha*, Spirotrichosoma*, Staurojoenina, Teranympha, Trichonympha, Urinympha.
 * Preaxostyla
 * Oxymonadida . Barroella, Blattamonas, Brachymonas, Dinenympha, Microrhopalodina, Monocercomonoides, Notila, Opisthomitus, Oxymonas, Paranotila, Polymastix, Pyrsonympha, Sauromonas, Saccinobaculus, Streblomastix, Tubulimonoides.
 * Trimastigidae . Trimastix.
 * Paratrimastigidae . Paratrimastix.

Discoba {{au|Simpson in Hampl et al. 2009}}

 * Jakobida
 * Ophirinina
 * Agogonidae . Agogonia.
 * Ophirinidae . Ophirina.
 * Andalucina
 * Andaluciidae . Andalucia.
 * Stygiellidae . Stygiella, Velundella.
 * Histionina . Histiona, Jakoba, Moramonas, Reclinomonas, Seculamonas nomen nudum.
 * Tsukubamonadida . Tsukubamonas.
 * Heterolobosea [Percolozoa ]
 * Pharyngomonada . Pharyngomonas
 * Tetramitia
 * Selenaionidae . Dactylomonas, Selenaion.
 * Neovahlkampfiidae . Neovahlkampfia.
 * Eutetramitia
 * Vahlkampfiidae (P). Fumarolamoeba, Heteramoeba, Naegleria, Neovahlkampfia, Paravahlkampfia, Tetramitus, Vahlkampfia, Willaertia.
 * Gruberellidae . Gruberella*, Stachyamoeba.
 * Acrasidae . Acrasis, Allovahlkampfia, Pocheina.
 * Percolomonadidae . Percolomonas.
 * Psalteriomonadidae . Harpagon, Psalteriomonas, Monopylocystis, Pseudoharpagon, Sawyeria.
 * Stephanopogonidae . Stephanopogon.
 * Creneidae . Creneis.
 * Tulamoebidae . Pleurostomum, Tulamoeba.
 * Euglenozoa
 * Euglenida
 * Petalomonadida . Atraktomonas*, Biundula*, Calycimonas, Dolium, Dylakosoma*, Notosolenus, Pentamonas*, Petalomonas, Scytomonas, Sphenomonas, Tropidoscyphus*.
 * Alistosa . Ploeotia, Serpenomonas, Keelungia, Lentomonas, Decastava.
 * Entosiphon
 * Gaulosia
 * Karavia . Hemiolia, Liburna.
 * Olkaspira.
 * Chelandium
 * Olkasia
 * Spirocuta [Helicales ]
 * Anisonemia
 * Anisonemidae . Anisonema, Dinema (P), Heteronema.
 * Natomonadida
 * Neometanemidae . Neometanema.
 * Aphagea [Rhabdomonadina ]. Astasia, Distigma, Gyropaigne, Menoidium, Parmidium, Rhabdomonas.
 * Peranemidae (P). Chasmostoma, Jenningsia [Peranemopsis], Peranema, Teloprocta, Urceolus [Urceolopsis, Phialonema].
 * Euglenophyceae [Euglenea ]
 * Rapaza
 * Eutreptiales . Eutreptia, Eutreptiella.
 * Euglenales
 * Phacaceae . Discoplastis, Lepocinclis, Phacus.
 * Euglenaceae . Ascoglena, Colacium, Cryptoglena, Euglena, Euglenaformis, Euglenamorpha, Euglenaria, Euglenopsis, Hegneria, Klebsina, Monomorphina, Strombomonas, Trachelomonas.
 * Diplonemea
 * Diplonemidae . Diplonema, Rhynchopus, Lacrimia, Sulcionema, Flectonema.
 * Hemistasiidae . Hemistasia.
 * Eupelagonemidae . Eupelagonema.
 * Symbiontida . Bihospites, Calkinsia, Postgaardi.
 * Kinetoplastea . Incertae sedis genera: ?Bordnamonas, ?Cephalothamnium, ?Rhynchoidomonas.
 * Prokinetoplastina . Ichthyobodo, Perkinsela.
 * Metakinetoplastina
 * Neobodonida . Actuariola, Avlakibodo, Azumiobodo, Cruzella, Cryptaulax, Dimastigella, Klosteria, Neobodo, Phanerobia, Rhynchobodo, Rhynchomonas.
 * Parabodonida . Cryptobia, Jarrellia, Parabodo, Procryptobia, Trypanoplasma.
 * Eubodonida . Bodo.
 * Trypanosomatida . Angomonas, Blechomonas, Leptomonas, Paratrypanosoma, Sergeia, Strigomonas, Wallaceina, Phytomonas, Trypanosoma.
 * Leishmaniinae . Borovskyia, Crithidia, Leptomonas, Lotmaria, Novymonas, Porcisia, Zelonia, Endotrypanum, Leishmania.

CRuMs {{au|Brown et al. 2018}}

 * Collodictyonidae [Diphylleidae ; Diphylleida ; Diphyllatea, Sulcomonadidae ]. Collodictyon, Diphylleia [Aulacomonas], Sulcomonas.
 * Rigifilida [Hilomonadea ]
 * Micronucleariidae . Micronuclearia.
 * Rigifilidae . Rigifila.
 * Mantamonadidae [Glissodiscea ; Mantamonadida ]. Mantamonas.

Ancyromonadida {{au|Cavalier-Smith 1998}}

 * Ancyromonadidae . Ancyromonas, Nutomonas.
 * Planomonadidae . Fabomonas, Planomonas.

Genera of uncertain affiliation
Acinetactis, Actinastrum, Actinocoma, Actinolophus, Adinomonas, Aletium, Amphimonas, Amylophagus, Aphelidiopsis, Asterocaelum, Asthmatos, Aurospora, Barbetia, Berkeleyaesol, Belaria, Belonocystis, Bertarellia, Bertramia, Bodopsis, Boekelovia, Branchipocola, Camptoptyche, Chalarodora, Cibdelia, Cichkovia, Cinetidomyxa, Cingula, Cladomonas, Clathrella, Codonoeca, Coelosporidium, Copromonas, Cyanomastix, Cyclomonas, Cytamoeba, Dallingeria, Dictyomyxa, Dimastigamoeba, Dinemula, Dinoasteromonas, Diplocalium, Diplomita, Diplophysalis, Diploselmis, Dobellina, Ducelleria, Ectobiella, Elaeorhanis, Embryocola, Endamoeba, Endemosarca, Endobiella, Endomonas, Endospora, Enteromyxa, Eperythrocytozoon, Errera, Fromentella, Gweamonas, Gymnococcus, Gymnophrydium, Haematotractidium, Hartmannina, Heliobodo, Heliomonas, Hermisenella, Heterogromia, Hillea, Hyalodaktylethra, Immanoplasma, Isoselmis, Janickina, Kamera, Lagenidiopsis, Liegeosia, Luffisphaera, Lymphocytozoon, Lymphosporidium, Macappella, Magosphaera, Malpighiella, Martineziella, Megamoebomyxa, Meringosphaera, Microcometes, Monochrysis, Monodus, Mononema, Myrmicisporidium, Naupliicola, Nephrodinium, Neurosporidium, Orbulinella, Ovicola, Palisporomonas, Pansporella, Paradinemula, Parakaryon, Paraluffisphaera, Paramonas, Paraplasma, Parastasia, Parastasiella, Peliainia, Peltomonas, Petasaria, Phagodinium, Phanerobia, Phloxamoeba, Phyllomitus, Phyllomonas, Physcosporidium, Pleuophrys, Pleuromastix, Protenterospora, Protomonas, Pseudoactiniscus, Pseudosporopsis, Rhizomonas, Rhynchodinium, Rigidomastix, Schewiakoffia, Sergentella, Serpentoplasma, Sphaerasuctans, Spongastericus, Spongocyclia, Stephanomonas, Strobilomonas, Tetradimorpha, Tetragonidium, Thaulirens, Topsentella, Toshiba, Trichonema, Urbanella.