List of freshwater fish of Japan

This list of freshwater fish recorded in Japan is primarily based on the IUCN Red List, which, for fish found in inland waters, details the conservation status of some two hundred and sixty-one species, seventy-three of them endemic. Of these, one is assessed as extinct in the wild (the endemic Black kokanee), seven as critically endangered (the Sakhalin sturgeon, Chinese sturgeon, Sakhalin taimen, and endemic Tango stripe spined loach, Kissing loach, Cave goby, and Urauchi-isohaze), twenty as endangered, twelve as vulnerable, ten as near threatened, one hundred and seventy-nine as of least concern, and thirty-two as data deficient. This total includes species such as the Immaculate puffer, which, according to the IUCN Red List, may be characterized as a "marine species which occurs in estuaries...but is not dependent on these systems".

According to statistics accompanying the 2020 Japanese Ministry of the Environment (MoE) Red List, and the 2014 Red Data Book, approximately four hundred species and subspecies of freshwater fish and brackish water fish are to be found, but the conservation status of only two hundred and forty-five is detailed. Of these, three taxa are extinct from a domestic perspective (the Green sturgeon, Short ninespine stickleback, and endemic Suwa gudgeon), one extinct in the wild (the endemic Black kokanee), seventy-one critically endangered, fifty-four endangered, forty-four vulnerable, thirty-five near threatened, and thirty-seven data deficient. As of January 2021, for their protection, ten species and subspecies have been designated National Endangered Species by Cabinet Order in accordance with the 1992 Act on Conservation of Endangered Species of Wild Fauna and Flora.

A 2017 study, drawing on the 2013 edition of Fishes of Japan (日本産魚類検索), edited by Nakabo Tetsuji, and the 2001 edition of Freshwater Fishes of Japan (日本の淡水魚), edited by Kawanabe Hiroya, and including only those that "largely spend their lives in freshwater or diadromous fishes that reproduce in freshwater", but excluding those of the Ryūkyū Islands, lists some one hundred and eighty-one taxa, thirty-one of which, though they may have an established Japanese name and be written about at some length, are yet to be formally described, and as yet have no scientific binomial or trinomial. As for the inland water fishes of the Ryūkyūs, a 2014 checklist detailed some 678 species, in 110 families, and 27 orders, but of these, 334 are primarily marine species "but accidentally migrate to inland waters", with a further 229 estuarine species (143 residential, 86 peripheral), 59 species being fluvial, and 56 diadromous. In addition, it is noted that most of the fluvial species on Okinawa Island are alien. A 1998 study, drawing on earlier editions of the above works by Nakabo and Kawanabe, lists 211 taxa nationwide, in 35 families, and 15 orders, comprising 134 fluvial and lacustrine fishes (63%) and 77 diadromous fishes (37%), including 88 endemics (41%) and 23 exotics (11%).

As of the 7 July 2021 update, Eschmeyer's Catalog of Fishes returns three hundred and forty species records for freshwater fishes of Japan, excluding synonyms unless valid as a subspecies, and four hundred and thirty-two brackish water fishes, one hundred and ninety-two records representing those found in both systems, one hundred and fifty-six of which are also found in marine environments.

Other than the lampreys with which the list begins, which are jawless fish, all orders are within the clade Actinopterygii, ray-finned fishes.

Order: Petromyzontiformes

 * Family: Petromyzontidae
 * Genus: Entosphenus
 * Pacific lamprey, Entosphenus tridentatus
 * Genus: Lethenteron
 * Arctic lamprey, Lethenteron camtschaticum (MoE: VU (as Lethenteron japonicum))
 * Siberian brook lamprey, Lethenteron kessleri(MoE: NT)
 * Far Eastern brook lamprey, Lethenteron reissneri

Order: Acipenseriformes

 * Family: Acipenseridae
 * Genus: Acipenser
 * Green sturgeon, Acipenser medirostris (MoE: EX)
 * Sakhalin sturgeon, Acipenser mikadoi
 * Chinese sturgeon, Acipenser sinensis

Order: Anguilliformes

 * Family: Anguillidae
 * Genus: Anguilla
 * Shortfin eel, Anguilla bicolor
 * Indian shortfin eel, A. b. pacifica(MoE: DD)
 * Japanese eel, Anguilla japonica (MoE: EN)
 * Marbled eel, Anguilla marmorata
 * Family: Muraenesocidae
 * Genus: Muraenesox
 * Daggertooth pike conger, Muraenesox cinereus
 * Family: Muraenidae
 * Genus: Echidna
 * Pink-lipped moray eel, Echidna rhodochilus(MoE: CR)
 * Genus: Uropterygius
 * Brown moray eel, Uropterygius concolor (MoE: CR)

Order: Atheriniformes

 * Family: Atherinidae
 * Genus: Atherinomorus
 * Tropical silverside, Atherinomorus duodecimalis (MoE: DD)
 * Genus: Hypoatherina
 * Samoan silverside, Hypoatherina temminckii (MoE: DD)
 * Family: Atherinopsidae
 * Genus: Odontesthes
 * Argentinian silverside, Odontesthes bonariensis(introduced )

Order: Aulopiformes

 * Family: Synodontidae
 * Genus: Saurida
 * Clouded lizardfish, Saurida nebulosa

Order: Beloniformes

 * Family: Adrianichthyidae
 * Genus: Oryzias
 * Japanese rice fish, Oryzias latipes (endemic) (MoE: VU)
 * Kitanomedaka, Oryzias sakaizumii (endemic) (MoE: VU)
 * Family: Hemiramphidae
 * Genus: Hyporhamphus
 * Asian pencil halfbeak, Hyporhamphus intermedius(MoE: NT)
 * Family: Zenarchopteridae
 * Genus: Zenarchopterus
 * Duncker's river garfish, Zenarchopterus dunckeri (MoE: NT)

Order: Callionymiformes

 * Family: Callionymidae
 * Genus: Pseudocalliurichthys
 * Ryukyu ruddertail dragonet, Pseudocalliurichthys ikedai(MoE: DD)

Order: Clupeiformes

 * Family: Clupeidae
 * Genus: Clupea
 * Pacific herring, Clupea pallasii
 * Family: Engraulidae
 * Genus: Coilia
 * Japanese grenadier anchovy, Coilia nasus (MoE: EN)
 * Genus: Nematalosa
 * Western Pacific gizzard shad, Nematalosa come
 * Japanese gizzard shad, Nematalosa japonica (MoE: EN)
 * Bloch's gizzard shad, Nematalosa nasus
 * Genus: Thryssa
 * Baelama anchovy, Thryssa baelama

Order: Cypriniformes

 * Family: Cobitidae
 * Genus: Cobitis
 * Japanese striped loach, Cobitis biwae
 * Ajime loach, Cobitis delicata (endemic) (MoE: VU (as Niwaella delicata))
 * Ariake stripe spined loach, Cobitis kaibarai (endemic) (MoE: EN)
 * Large stripe spined loach, Cobitis magnostriata (endemic) (MoE: EN)
 * Yamato spined loach, Cobitis matsubarae (endemic) (MoE: VU)
 * Cobitis melanoleuca
 * Small stripe spined loach, Cobitis minamorii (endemic)
 * Sanyōkogatasuji-shimadojō, C. m. minamorii(MoE: CR)
 * Biwakogatasuji-shimadojō, C. m. oumiensis(MoE: EN)
 * Saninkogatasuji-shimadojō, C. m. saninensis(MoE: EN)
 * Tokaikogatasuji-shimadojō, C. m. tokaiensis(MoE: EN)
 * Yodokogatasuji-shimadojō, C. m. yodoensis(MoE: CR)
 * Oyodo stripe spined loach, Cobitis sakahoko (endemic) (MoE: EN)
 * Dwarf gravel loach, Cobitis shikokuensis (endemic) (MoE: EN)
 * Namisuji-shimadojō, Cobitis striata
 * Ongasuji-shimadojō, C. s. fuchigamii(MoE: EN)
 * Hakatasuji-shimadojō, C. s. hakataensis(MoE: CR)
 * Chūgatasuji-shimadojō, C. s. striata(MoE: VU)
 * Secret loach, Cobitis takatsuensis (endemic) (MoE: EN)
 * Tango stripe spined loach, Cobitis takenoi (endemic) (MoE: CR)
 * Genus: Misgurnus
 * Pond loach, Misgurnus anguillicaudatus (MoE: NT)
 * Genus: Parabotia
 * Kissing loach, Parabotia curtus (endemic) (MoE: CR)
 * Family: Cyprinidae
 * Genus: Abbottina
 * Chinese false gudgeon, Abbottina rivularis(endemic) (MoE: EN)
 * Genus: Acheilognathus
 * Striped bitterling, Acheilognathus cyanostigma (endemic) (MoE: CR)
 * Deepbodied bitterling, Acheilognathus longipinnis (endemic) (MoE: CR)
 * Giant Chinese bitterling, Acheilognathus macropterus (introduced )
 * Genuine bitterling, Acheilognathus melanogaster (endemic) (MoE: EN)
 * Flat bitterling, Acheilognathus rhombeus
 * Tabira bitterling, Acheilognathus tabira (endemic)
 * Red tabira bitterling, A. t. erythropterus(MoE: EN)
 * Southern red tabira bitterling, A. t. jordani(MoE: CR)
 * Blotched tabira bitterling, A. t. nakamurae(MoE: CR)
 * White tabira bitterling, A. t. tabira(MoE: EN)
 * Northern red tabira bitterling, A. t. tohokuensis(MoE: EN)
 * Metallic bitterling, Acheilognathus typus (endemic) (MoE: CR)
 * Genus: Aphyocypris
 * Chinese bleak, Aphyocypris chinensis (MoE: CR)
 * Genus: Biwia
 * Yodo gudgeon, Biwia yodoensis (endemic) (MoE: EN)
 * Biwa gudgeon, Biwia zezera (endemic) (MoE: VU)
 * Genus: Carassius
 * Goldfish, Carassius auratus
 * Round crucian carp, C. a. grandoculis(endemic) (MoE: EN (as Carassius buergeri grandoculis))
 * Japanese white crucian carp, Carassius cuvieri (MoE: EN)
 * Japanese silver crucian carp, Carassius langsdorfii
 * Genus: Ctenopharyngodon
 * Grass carp, Ctenopharyngodon idella(introduced )
 * Genus: Cyprinus
 * Common carp, Cyprinus carpio
 * Amur carp, Cyprinus rubrofuscus (introduced)
 * Genus: Danio
 * Pearl danio, Danio albolineatus (introduced on Okinawa Island )
 * Zebrafish, Danio rerio (introduced on Okinawa Island )
 * Genus: Gnathopogon
 * Biwa moroko gudgeon, Gnathopogon caerulescens (endemic) (MoE: CR)
 * Gnathopogon elongatus(endemic)
 * Field gudgeon, G. e. elongatus
 * Suwa gudgeon, G. e. suwae(MoE: EX)
 * Genus: Hemibarbus
 * Barbel steed, Hemibarbus barbus
 * Zunaganigoi, Hemibarbus longirostris
 * Genus: Hemiculter
 * Sharpbelly, Hemiculter leucisculus
 * Genus: Hemigrammocypris
 * Golden venus fish, Hemigrammocypris neglectus (endemic) (MoE: EN)
 * Genus: Hypophthalmichthys
 * Silver carp, Hypophthalmichthys molitrix (introduced )
 * Bighead carp, Hypophthalmichthys nobilis (introduced )
 * Genus: Ischikauia
 * Lakeweed chub, Ischikauia steenackeri (endemic) (MoE: CR)
 * Genus: Mylopharyngodon
 * Black carp, Mylopharyngodon piceus (introduced )
 * Genus: Nipponocypris
 * Numamutsu, Nipponocypris sieboldii
 * Dark chub, Nipponocypris temminckii
 * Genus: Opsariichthys
 * Chinese hook snout carp, Opsariichthys bidens
 * Amur three-lips, Opsariichthys uncirostris
 * Hasu, O. u. uncirostris(MoE: VU)
 * Genus: Paramisgurnus
 * Large-scale loach, Paramisgurnus dabryanus(introduced )
 * Genus: Pseudogobio
 * Pike gudgeon, Pseudogobio esocinus
 * Genus: Pseudorasbora
 * Topmouth gudgeon, Pseudorasbora parva
 * Ushimotsugo minnow, Pseudorasbora pugnax (endemic) (MoE: CR)
 * Shinai topmouth gudgeon, Pseudorasbora pumila (endemic) (MoE: CR)
 * Genus: Pungtungia
 * Black stripe gudgeon, Pungtungia herzi
 * Genus: Rhodeus
 * Kyushu bitterling, Rhodeus atremius (endemic)
 * Kyushu rose bitterling, R. a. atremius(MoE: EN)
 * Suigen rose bitterling, R. a. suigensis(MoE: CR)
 * Rosy bitterling, Rhodeus ocellatus
 * Japanese rose bitterling, R. o. kurumeus(MoE: CR)
 * Rose bitterling, R. o. ocellatus(introduced )
 * Genus: Rhynchocypris
 * Amur minnow, Rhynchocypris lagowskii
 * Japanese fat minnow, R. l. steindachneri
 * Yamanaka minnow, R. l. yamamotis(MoE: DD (as Phoxinus lagowskii yamamotis))
 * Chinese minnow, Rhynchocypris oxycephalus
 * Takahaya, R. o. jouyi
 * Lake minnow, Rhynchocypris percnurus
 * Sakhalin lake minnow, R. p. sachalinensis(MoE: NT (as Phoxinus percnurus sachalinensis))
 * Sakhalin minnow, Rhynchocypris sachalinensis
 * Genus: Sarcocheilichthys
 * Oily gudgeon, Sarcocheilichthys biwaensis (endemic) (MoE: CR)
 * Higai minnow, Sarcocheilichthys variegatus
 * Biwa minnow, S. v. microoculus
 * Kawa-higai, S. v. variegatus(MoE: NT)
 * Genus: Squalidus
 * Khanka gudgeon, Squalidus chankaensis
 * Sugo-moroko, S. c. biwae(MoE: VU)
 * Kōrai-moroko, S. c. tsuchigae
 * Squalidus gracilis
 * Itomoroko, S. g. gracilis
 * Squalidus japonicus
 * Japanese gudgeon, S. j. japonicus(MoE: VU)
 * Genus: Tanakia
 * Slender bitterling, Tanakia lanceolata (MoE: NT)
 * Oily bitterling, Tanakia limbata (endemic) (MoE: NT)
 * Tokyo bitterling, Tanakia tanago (endemic) (MoE: CR)
 * Genus: Tribolodon
 * Pacific redfin, Tribolodon brandtii
 * Jūsan-ugui, T. b. brandtii
 * Maruta [ja], T. b. maruta
 * Big-scaled redfin, Tribolodon hakonensis
 * Long lowerjaw dace, Tribolodon nakamurai (endemic) (MoE: EN)
 * Rosyface dace, Tribolodon sachalinensis
 * Genus: Zacco
 * Freshwater minnow, Zacco platypus
 * Family: Nemacheilidae
 * Genus: Barbatula
 * Barbatula oreas
 * Siberian stone loach, Barbatula toni
 * Genus: Lefua
 * Japanese eight barbel loach, Lefua echigonia (endemic) (MoE: EN)
 * Ainu eight barbel loach, Lefua nikkonis (endemic) (MoE: EN (as Lefua costata nikkonis))
 * Tōkainagare-hotokedojō, Lefua tokaiensis(endemic) (MoE: EN)
 * Nagare-hotokedojō, Lefua torrentis(endemic) (MoE: EN)

Order: Cyprinodontiformes

 * Family: Poeciliidae
 * Genus: Gambusia
 * Mosquitofish, Gambusia affinis (introduced )
 * Genus: Poecilia
 * Guppy, Poecilia reticulata (introduced )
 * Molly, Poecilia sphenops (introduced in Hokkaidō )
 * Genus: Xiphophorus
 * Green swordtail, Xiphophorus hellerii (introduced )
 * Southern platyfish, Xiphophorus maculatus (introduced on Okinawa Island but population possibly extinct )

Order: Elopiformes

 * Family: Elopidae
 * Genus: Elops
 * Ten-pounder, Elops machnata
 * Family: Megalopidae
 * Genus: Megalops
 * Indo-Pacific tarpon, Megalops cyprinoides

Order: Gasterosteiformes

 * Family: Gasterosteidae
 * Genus: Gasterosteus
 * Three-spined stickleback, Gasterosteus aculeatus
 * Smallhead stickleback, Gasterosteus microcephalus
 * Japan Sea stickleback, Gasterosteus nipponicus
 * Genus: Pungitius
 * Short ninespine stickleback, Pungitius kaibarae(MoE: EX)
 * Ninespine stickleback, Pungitius pungitius
 * Amur stickleback, Pungitius sinensis
 * Sakhalin stickleback, Pungitius tymensis (MoE: VU)

Order: Gonorynchiformes

 * Family: Chanidae
 * Genus: Chanos
 * Milkfish, Chanos chanos

Order: Mugiliformes

 * Family: Mugilidae
 * Genus: Cestraeus
 * Lobed river mullet, Cestraeus plicatilis (MoE: CR)
 * Genus: Chelon
 * Otomebora mullet, Chelon melinopterus
 * Greenback mullet, Chelon subviridis (MoE: DD)
 * Genus: Ellochelon
 * Squaretail mullet, Ellochelon vaigiensis (MoE: DD)
 * Genus: Crenimugil
 * Fringelip mullet, Crenimugil crenilabis
 * Half fringelip mullet, Crenimugil heterocheilos (MoE: EN)
 * Longfin mullet, Crenimugil pedaraki(MoE: DD (as Moolgarda pedaraki))
 * Bluespot mullet, Crenimugil seheli
 * Genus: Osteomugil
 * Monnashibora, Osteomugil engeli (MoE: DD (as Moolgarda engeli))
 * Genus: Planiliza
 * Largescale mullet, Planiliza macrolepis
 * Genus: Valamugil
 * Bluetail mullet, Valamugil buchanani

Order: Osmeriformes

 * Family: Osmeridae
 * Genus: Hypomesus
 * Japanese smelt, Hypomesus nipponensis
 * Pond smelt, Hypomesus olidus (MoE: NT)
 * Genus: Osmerus
 * Arctic rainbow smelt, Osmerus dentex
 * Family: Plecoglossidae
 * Genus: Plecoglossus
 * Sweetfish, Plecoglossus altivelis
 * Ayu, P. a. altivelis
 * Ryukyu ayu, P. a. ryukyuensis(endemic) (MoE: CR)
 * Genus: Spirinchus
 * Shishamo smelt, Spirinchus lanceolatus
 * Family: Salangidae
 * Genus: Neosalanx
 * Ariake dwarf icefish, Neosalanx reganius (endemic) (MoE: CR)
 * Genus: Salanx
 * Ariake icefish, Salanx ariakensis(MoE: CR)

Order: Perciformes

 * Family: Ambassidae
 * Genus: Ambassis
 * Malabar glassy perchlet, Ambassis dussumieri
 * Long-spined glassfish, Ambassis interrupta (MoE: DD)
 * Estuarine glass perchlet, Ambassis macracanthus (MoE: DD)
 * Flag-tailed glassfish, Ambassis miops
 * Bleeker's glass perchlet, Ambassis urotaenia
 * Vachell's glassfish, Ambassis vachellii
 * Genus: Pseudambassis
 * Indian glassy fish, Pseudambassis ranga (introduced on Okinawa Island )
 * Family: Apogonidae
 * Genus: Apogon
 * Ambon cardinalfish, Apogon amboinensis
 * Genus: Ostorhinchus
 * Humpback cardinalfish, Ostorhinchus lateralis (MoE: DD (as Fibramia lateralis))
 * Genus: Pseudamia
 * White-jawed cardinalfish, Pseudamia amblyuroptera(MoE: DD)
 * Genus: Yarica
 * Mangrove cardinalfish, Yarica hyalosoma (MoE: CR)
 * Family: Blenniidae
 * Genus: Omobranchus
 * Chevroned blenny, Omobranchus elongatus (MoE: DD)
 * Gossamer blenny, Omobranchus ferox (MoE: CR)
 * Genus: Omox
 * Omox blenny, Omox biporos (MoE: CR)
 * Family: Carangidae
 * Genus: Caranx
 * Bigeye trevally, Caranx sexfasciatus
 * Family: Centrarchidae
 * Genus: Lepomis
 * Bluegill, Lepomis macrochirus (introduced )
 * Genus: Micropterus
 * Smallmouth bass, Micropterus dolomieu (introduced )
 * Largemouth bass, Micropterus salmoides (introduced )
 * Family: Channidae
 * Genus: Channa
 * Northern snakehead, Channa argus(introduced )
 * Small snakehead, Channa asiatica (introduced )
 * Blotched snakehead, Channa maculata (introduced )
 * Family: Cichlidae
 * Genus: Amatitlania
 * Convict cichlid, Amatitlania nigrofasciata (introduced )
 * Genus: Oreochromis
 * Mozambique tilapia, Oreochromis mossambicus (introduced )
 * Nile tilapia, Oreochromis niloticus (introduced )
 * Genus: Otopharynx
 * Otopharynx lithobates (introduced on Okinawa Island )
 * Genus: Tilapia
 * Redbelly tilapia, Tilapia zillii (introduced )
 * Family: Eleotridae
 * Genus: Belobranchus
 * Throat-spine gudgeon, Belobranchus belobranchus (MoE: DD)
 * Genus: Bostrychus
 * Four-eyed sleeper, Bostrychus sinensis (MoE: EN)
 * Genus: Bunaka
 * Green-backed gudgeon, Bunaka gyrinoides (MoE: NT)
 * Genus: Butis
 * Ambon gudgeon, Butis amboinensis (MoE: CR)
 * Crimson-tipped gudgeon, Butis butis
 * Genus: Eleotris
 * Spine-cheek gudgeon, Eleotris acanthopomus
 * Brown spine-cheek gudgeon, Eleotris fusca
 * Broadhead sleeper, Eleotris melanosoma
 * Spined sleeper, Eleotris oxycephala
 * Genus: Eugnathogobius
 * Stripe-face calamiana, Eugnathogobius mindora (MoE: NT)
 * Genus: Hypseleotris
 * Tropical carp-gudgeon, Hypseleotris cyprinoides (MoE: EN)
 * Genus: Ophiocara
 * Spangled gudgeon, Ophiocara porocephala (MoE: VU)
 * Family: Epinephelidae
 * Genus: Epinephelus
 * Palemargin grouper, Epinephelus bontoides (MoE: DD)
 * Family: Gerreidae
 * Genus: Gerres filamentosus
 * Threadfin silverbelly, Gerres filamentosus
 * Family: Gobiidae
 * Genus: Acanthogobius
 * Yellowfin goby, Acanthogobius flavimanus
 * Spear-like Oriental goby, Acanthogobius hasta (endemic) (MoE: VU)
 * Minami-ashishirohaze, Acanthogobius insularis (endemic) (MoE: VU)
 * Genus: Acentrogobius
 * Mangrove goby, Acentrogobius audax (MoE: NT)
 * Tropical sand goby, Acentrogobius caninus (MoE: NT)
 * Robust mangrove goby, Acentrogobius janthinopterus
 * Sulu goby, Acentrogobius suluensis(MoE: NT)
 * Spotted green goby, Acentrogobius viridipunctatus (MoE: VU)
 * Genus: Amblygobius
 * Link's goby, Amblygobius linki (MoE: NT)
 * Genus: Apocryptodon
 * Spotted hidden-teeth goby, Apocryptodon punctatus (endemic) (MoE: VU)
 * Genus: Awaous
 * Scribbled goby, Awaous grammepomus
 * Largesnout goby, Awaous melanocephalus
 * Ocellated river goby, Awaous ocellaris
 * Genus: Bathygobius
 * Brown frillfin, Bathygobius fuscus
 * Genus: Boleophthalmus
 * Great blue-spotted mudskipper, Boleophthalmus pectinirostris(MoE: EN)
 * Genus: Caragobius
 * Scaleless worm goby, Caragobius urolepis (MoE: VU)
 * Genus: Chaenogobius
 * Agohaze, Chaenogobius annularis
 * Genus: Cristatogobius
 * Hime-tosakahaze, Cristatogobius aurimaculatus(MoE: CR)
 * Tosakahaze, Cristatogobius lophius(MoE: EN)
 * Kuro-tosakahaze, Cristatogobius nonatoae(MoE: CR)
 * Genus: Eutaeniichthys
 * Brackish water goby, Eutaeniichthys gilli(MoE: NT)
 * Genus: Eviota
 * Urauchi-isohaze, Eviota ocellifer (endemic) (MoE: CR)
 * Genus: Exyrias
 * Puntang goby, Exyrias puntang
 * Genus: Favonigobius
 * Indo-pacific tropical sand goby, Favonigobius reichei
 * Genus: Glossogobius
 * Golden flathead goby, Glossogobius aureus (MoE: CR)
 * Bearded flathead goby, Glossogobius bicirrhosus (MoE: CR)
 * Circumspect goby, Glossogobius circumspectus (MoE: NT)
 * Bareye goby, Glossogobius giuris
 * Iwahaze, Glossogobius illimis
 * Urohaze goby, Glossogobius olivaceus
 * Genus: Gobiodon
 * Rippled coral goby, Gobiodon rivulatus
 * Genus: Gymnogobius
 * Biringo, Gymnogobius breunigii
 * Chestnut goby, Gymnogobius castaneus (MoE: NT)
 * Kiseruhaze, Gymnogobius cylindricus (endemic) (MoE: EN)
 * Biwa goby, Gymnogobius isaza (endemic) (MoE: CR)
 * Edo-haze, Gymnogobius macrognathos(MoE: VU)
 * Hebihaze, Gymnogobius mororanus(MoE: DD)
 * Koshinohaze, Gymnogobius nakamurae(MoE: CR)
 * Sumiukigori, Gymnogobius petschiliensis
 * Kubohaze, Gymnogobius scrobiculatus (endemic) (MoE: EN)
 * Shinjiko-haze, Gymnogobius taranetzi (MoE: VU)
 * Chikuzen-haze, Gymnogobius uchidai (endemic) (MoE: VU)
 * Shima-ukigori, Gymnogobius opperiens
 * Floating goby, Gymnogobius urotaenia
 * Genus: Gobitrichinotus
 * Sand fish, Gobitrichinotus radiocularis (MoE: NT)
 * Genus: Istigobius
 * Ornate goby, Istigobius ornatus
 * Genus: Lentipes
 * Yoroi-bōzuhaze, Lentipes armatus(MoE: CR)
 * Genus: Leucopsarion
 * Ice goby, Leucopsarion petersii(MoE: VU)
 * Genus: Luciogobius
 * Cave goby, Luciogobius albus (endemic) (MoE: CR)
 * Nemuri-mimizuhaze, Luciogobius dormitoris (endemic) (MoE: DD)
 * Nagare-mimizuhaze, Luciogobius fluvialis (endemic) (MoE: NT)
 * Yusui-mimizuhaze, Luciogobius fonticola (endemic) (MoE: NT)
 * Flathead goby, Luciogobius guttatus
 * Well goby, Luciogobius pallidus (endemic) (MoE: NT)
 * Minamihime-mimizuhaze, Luciogobius ryukyuensis (endemic) (MoE: VU)
 * Genus: Mangarinus
 * Uchiwahaze, Mangarinus waterousi
 * Genus: Mugilogobius
 * Bandfin mangrove goby, Mugilogobius cavifrons (MoE: EN)
 * Yellowstripe goby, Mugilogobius chulae
 * Dusky mangrove goby, Mugilogobius fuscus (MoE: DD)
 * Merton's mangrove goby, Mugilogobius mertoni (MoE: VU)
 * Genus: Odontamblyopus
 * Warasubo, Odontamblyopus lacepedii(MoE: VU)
 * Genus: Oligolepis
 * Sharptail goby, Oligolepis acutipennis
 * Plain teardrop goby, Oligolepis stomias
 * Genus: Oxyurichthys
 * Shimasaruhaze, Oxyurichthys takagi (MoE: CR)
 * Genus: Pandaka
 * Lidwill's dwarf goby, Pandaka lidwilli(MoE: VU)
 * Genus: Parkraemeria
 * Ginpohaze, Parkraemeria saltator (endemic) (MoE: VU)
 * Genus: Periophthalmus
 * Barred mudskipper, Periophthalmus argentilineatus
 * Shuttles mudskipper, Periophthalmus modestus(MoE: NT)
 * Genus: Psammogobius
 * Sleepy goby, Psammogobius biocellatus
 * Genus: Pseudapocryptes
 * Hokohaze, Pseudapocryptes elongatus
 * Genus: Pseudogobius
 * Masagohaze, Pseudogobius masago(MoE: VU)
 * Black-spotted goby, Pseudogobius melanosticta (MoE: DD (as Pseudogobius gastrospilos))
 * Northern fatnose goby, Pseudogobius poicilosoma
 * Genus: Redigobius
 * Girdled goby, Redigobius balteatus (endemic) (MoE: DD)
 * Speckled goby, Redigobius bikolanus
 * Genus: Rhinogobius
 * Biwa yellow-gill goby, Rhinogobius biwaensis (endemic) (MoE: DD)
 * Amur goby [es], Rhinogobius brunneus
 * Lizard goby, Rhinogobius flumineus
 * Ō-yoshinobori, Rhinogobius fluviatilis
 * Barcheek goby, Rhinogobius giurinus
 * Orange Amur goby, Rhinogobius kurodai
 * Hori-yoshinobori, Rhinogobius mizunoi
 * Shima-yoshinobori, Rhinogobius nagoyae
 * Ogasawara freshwater goby, Rhinogobius ogasawaraensis (endemic) (MoE: EN)
 * Tōkai-yoshinobori, Rhinogobius telma(MoE: NT)
 * Shimahire-yoshinobori, Rhinogobius tyoni(MoE: NT)
 * Genus: Scartelaos
 * Walking goby, Scartelaos histophorus (MoE: CR)
 * Genus: Schismatogobius
 * Shima-esohaze, Schismatogobius ampluvinculus (MoE: EN)
 * Kaeru-esohaze, Schismatogobius marmoratus
 * Esohaze, Schismatogobius roxasi (MoE: EN)
 * Genus: Sicyopterus
 * Grazing goby, Sicyopterus japonicus
 * Red-tailed goby, Sicyopterus lagocephalus (MoE: VU)
 * Sicyopterus macrostetholepis'
 * Genus: Sicyopus
 * Hinokoromo-bōzuhaze, Sicyopus auxilimentus (MoE: DD)
 * Aka-bōzuhaze, Sicyopus zosterophorus (MoE: CR)
 * Genus: Silhouettea
 * Shiranui-haze, Silhouettea dotui (endemic) (MoE: NT)
 * Genus: Smilosicyopus
 * Kaeru-haze, Smilosicyopus leprurus (endemic) (MoE: CR)
 * Genus: Stenogobius
 * Dōke-haze, Stenogobius ophthalmoporus (MoE: DD)
 * Genus: Stiphodon
 * Hisui-bōzuhaze, Stiphodon alcedo(MoE: CR)
 * Konteri-bōzuhaze, Stiphodon atropurpureus (MoE: CR)
 * Hayase-bōzuhaze, Stiphodon imperiorientis (endemic) (MoE: CR)
 * Torafu-bōzuhaze, Stiphodon multisquamus (MoE: DD)
 * Niraikanai-bōzuhaze, Stiphodon niraikanaiensis(MoE: DD)
 * Nanyō-bōzuhaze, Stiphodon percnopterygionus
 * Kakiirohime-bōzuhaze, Stiphodon surrufus (MoE: DD)
 * Genus: Taenioides
 * Eel worm goby, Taenioides anguillaris
 * Whiskered eel goby, Taenioides cirratus (MoE: EN)
 * Genus: Tridentiger
 * Shokihaze goby, Tridentiger barbatus(MoE: NT)
 * Short-spined Japanese trident goby, Tridentiger brevispinis
 * Shimofuri goby, Tridentiger bifasciatus
 * Naganogori, Tridentiger kuroiwae (endemic)
 * Bare-naped goby, Tridentiger nudicervicus(MoE: NT)
 * Japanese trident goby, Tridentiger obscurus
 * Chameleon goby, Tridentiger trigonocephalus
 * Genus: Trypauchen
 * Indo-Pacific burrowing goby, Trypauchen vagina
 * Genus: Trypauchenopsis
 * Bearded eel goby, Trypauchenopsis intermedia (MoE: VU)
 * Genus: Yongeichthys
 * Shadow goby, Yongeichthys nebulosus
 * Family: Haemulidae
 * Genus: Plectorhinchus
 * Giant sweetlips, Plectorhinchus albovittatus(MoE: DD)
 * Brown sweetlips, Plectorhinchus gibbosus
 * Family: Kraemeriidae
 * Genus: Kraemeria
 * Tonga-sunahaze, Kraemeria tongaensis (MoE: DD)
 * Family: Kuhliidae
 * Genus: Kuhlia
 * Dark-margined flagtail, Kuhlia marginata
 * Five-bar flagtail, Kuhlia mugil
 * Silver flagtail, Kuhlia munda (MoE: EN)
 * Jungle perch, Kuhlia rupestris
 * Family: Lateolabracidae
 * Genus: Lateolabrax
 * Japanese sea bass, Lateolabrax japonicus
 * Family: Latidae
 * Genus: Lates
 * Barramundi, Lates calcarifer
 * Japanese barramundi, Lates japonicus (endemic) (MoE: EN)
 * Family: Leiognathidae
 * Genus: Aurigequula
 * Striped ponyfish, Aurigequula fasciata
 * Genus: Equulites
 * Whipfin ponyfish, Equulites leuciscus
 * Genus: Eubleekeria
 * Splendid ponyfish, Eubleekeria splendens
 * Genus: Gazza
 * Toothed ponyfish, Gazza minuta
 * Genus: Leiognathus
 * Common ponyfish, Leiognathus equulus
 * Family: Lutjanidae
 * Genus: Lutjanus
 * Blackspot snapper, Lutjanus ehrenbergii
 * Blacktail snapper, Lutjanus fulvus
 * Papuan black snapper, Lutjanus goldiei(MoE: CR)
 * Family: Microdesmidae
 * Genus: Parioglossus
 * Kujakuhaze, Parioglossus caeruleolineatus (endemic) (MoE: DD)
 * Beautiful hover goby, Parioglossus formosus
 * Blackstripe dartfish, Parioglossus lineatus (MoE: DD)
 * Interrupted dartfish, Parioglossus interruptus(MoE: CR)
 * Estuarine dartfish, Parioglossus palustris (MoE: VU)
 * Rainford's dartfish, Parioglossus rainfordi (MoE: EN)
 * Yellow dartfish, Parioglossus raoi
 * Striped dartfish, Parioglossus taeniatus (MoE: CR)
 * Family: Monodactylidae
 * Genus: Monodactylus
 * Silver moony, Monodactylus argenteus
 * Family: Odontobutidae
 * Genus: Micropercops
 * Yokoshima-donko, Micropercops swinhonis
 * Genus: Odontobutis
 * Ishi-donko, Odontobutis hikimius (endemic) (MoE: VU)
 * Dark sleeper, Odontobutis obscura
 * Family: Osphronemidae
 * Genus: Macropodus
 * Round-tailed paradise fish, Macropodus ocellatus(introduced )
 * Paradise fish, Macropodus opercularis (introduced? ) (MoE: CR)
 * Family: Pomacentridae
 * Genus: Pomacentrus
 * River damsel, Pomacentrus taeniometopon
 * Family: Rhyacichthyidae
 * Genus: Rhyacichthys
 * Loach goby, Rhyacichthys aspro (MoE: CR)
 * Family: Scatophagidae
 * Genus: Scatophagus
 * Spotted scat, Scatophagus argus
 * Family: Scombridae
 * Genus: Scomberomorus
 * Chinese mackerel, Scomberomorus sinensis
 * Family: Sillaginidae
 * Genus: Sillaginops
 * Large-scale whiting, Sillaginops macrolepis(MoE: EN)
 * Genus: Sillago
 * Small-scale whiting, Sillago parvisquamis (MoE: CR)
 * Family: Sinipercidae
 * Genus: Coreoperca
 * Japanese perch, Coreoperca kawamebari(MoE: EN)
 * Family: Sparidae
 * Genus: Acanthopagrus
 * Yellowfin seabream, Acanthopagrus latus
 * Pacific seabream, Acanthopagrus pacificus (MoE: VU)
 * Okinawa seabream, Acanthopagrus sivicolus
 * Family: Terapontidae
 * Genus: Mesopristes
 * Silver grunter, Mesopristes argenteus (MoE: CR)
 * Tapiroid grunter, Mesopristes cancellatus (MoE: CR)
 * Shimizu-shimaisaki, Mesopristes iravi (MoE: CR)
 * Genus: Terapon
 * Tiger perch, Terapon jarbua
 * Family: Toxotidae
 * Genus: Toxotes
 * Banded archerfish, Toxotes jaculatrix (MoE: CR)
 * Family: Tripterygiidae
 * Genus: Enneapterygius
 * Urauchi-hebiginpo, Enneapterygius cheni (MoE: CR)

Order: Pleuronectiformes

 * Family: Pleuronectidae
 * Genus: Platichthys
 * Starry flounder, Platichthys stellatus
 * Family: Soleidae
 * Genus: Brachirus
 * Oriental sole, Brachirus orientalis 

Order: Salmoniformes

 * Family: Salmonidae
 * Genus: Hucho
 * Sakhalin taimen, Hucho perryi (MoE: EN)
 * Genus: Oncorhynchus
 * Pink salmon, Oncorhynchus gorbuscha
 * Iwame trout, Oncorhynchus iwame (endemic)
 * Kunimasu, Oncorhynchus kawamurae (endemic) (MoE: EW)
 * Chum salmon, Oncorhynchus keta
 * Masu salmon, Oncorhynchus masou
 * Red-spotted masu salmon, O. m. ishikawae (MoE: NT)
 * Cherry salmon, O. m. masou (MoE: NT)
 * Rainbow trout, Oncorhynchus mykiss(introduced )
 * Sockeye salmon, Oncorhynchus nerka (MoE: CR)
 * Biwa trout, Oncorhynchus rhodurus
 * Genus: Salmo
 * Brown trout, Salmo trutta (introduced )
 * Genus: Salvelinus
 * Brook trout, Salvelinus fontinalis(introduced )
 * Kirikuchi char, Salvelinus japonicus (endemic)
 * White-spotted charr, Salvelinus leucomaenis
 * Head-spotted charr, S. l. imbrius(MoE: VU)
 * Japanese charr, S. l. japonicus
 * Amemasu, S. l. leucomaenis
 * Nikkō-iwana, S. l. pluvius(MoE: DD)
 * Dolly Varden trout, Salvelinus malma
 * Oshorokoma, S. m. krascheninnikovi(MoE: VU)
 * Northern Dolly Varden, S. m. malma
 * Miyabe charr, S. m. miyabei(MoE: VU)
 * Lake trout, Salvelinus namaycush(introduced )

Order: Scorpaeniformes

 * Family: Cottidae
 * Genus: Cottus
 * Sakhalin sculpin, Cottus amblystomopsis
 * Cherskii's sculpin, Cottus czerskii
 * Tyuman-river sculpin, Cottus hangiongensis
 * Fourspine sculpin, Cottus kazika (endemic) (MoE: VU)
 * Wrinklehead sculpin, Cottus nozawae
 * Japanese fluvial sculpin, Cottus pollux (endemic) (MoE: NT)
 * Kajika small-egg-type, Cottus reinii (endemic) (MoE: EN)
 * Genus: Trachidermus
 * Roughskin sculpin, Trachidermus fasciatus(MoE: EN)
 * Family: Tetrarogidae
 * Genus: Tetraroge
 * Bearded roguefish, Tetraroge barbata (MoE: CR)
 * Freshwater waspfish, Tetraroge nigra (MoE: CR)
 * Family: Triglidae
 * Genus: Chelidonichthys
 * Bluefin gurnard, Chelidonichthys kumu

Order: Siluriformes

 * Family: Amblycipitidae
 * Genus: Liobagrus
 * Reddish bullhead, Liobagrus reinii (endemic) (MoE: VU)
 * Family: Bagridae
 * Genus: Leiocassis
 * Chinese longsnout catfish, Leiocassis longirostris
 * Genus: Tachysurus
 * Ariake cuttailed bullhead, Tachysurus aurantiacus (endemic) (MoE: VU)
 * Korean bullhead, Tachysurus fulvidraco (introduced )
 * Stumpy bullhead, Tachysurus ichikawai (endemic) (MoE: EN)
 * Forktail bullhead, Tachysurus nudiceps
 * Cuttailed bullhead, Tachysurus tokiensis (endemic) (MoE: VU)
 * Family: Clariidae
 * Genus: Clarias
 * Walking catfish, Clarias batrachus (introduced )
 * Hong Kong catfish, Clarias fuscus (introduced )
 * Family: Ictaluridae
 * Genus: Ictalurus
 * Channel catfish, Ictalurus punctatus (introduced )
 * Family: Loricariidae
 * Genus: Pterygoplichthys
 * Vermiculated sailfin catfish, Pterygoplichthys disjunctivus(introduced on Okinawa Island )
 * Family: Siluridae
 * Genus: Silurus
 * Amur catfish, Silurus asotus
 * Lake Biwa catfish, Silurus biwaensis
 * Biwa rock catfish, Silurus lithophilus (endemic) (MoE: NT)

Order: Synbranchiformes

 * Family: Synbranchidae
 * Genus: Monopterus
 * Asian swamp eel, Monopterus albus
 * Oriental swamp eel, Monopterus javanensis

Order: Syngnathiformes

 * Family: Syngnathidae
 * Genus: Hippichthys
 * Bluespeckled pipefish, Hippichthys cyanospilos
 * Reticulated freshwater pipefish, Hippichthys heptagonus (MoE: EN)
 * Beady pipefish, Hippichthys penicillus
 * Bellybarred pipefish, Hippichthys spicifer
 * Genus: Microphis
 * Flat-nosed pipefish, Microphis argulus (MoE: CR)
 * Short-tailed pipefish, Microphis brachyurus
 * Philippine river pipefish, Microphis jagorii (MoE: CR)
 * Barhead pipefish, Microphis leiaspis
 * Ragged-tail pipefish, Microphis retzii (MoE: CR)
 * Genus: Syngnathus
 * Pacific seaweed pipefish, Syngnathus schlegeli

Order: Tetraodontiformes

 * Family: Tetraodontidae
 * Genus: Arothron
 * White-spotted puffer, Arothron hispidus
 * Immaculate puffer, Arothron immaculatus
 * Genus: Chelonodon
 * Milkspotted puffer, Chelonodon patoca
 * Genus: Lagocephalus
 * Silver-cheeked toadfish, Lagocephalus sceleratus
 * Genus: Takifugu
 * Grass puffer, Takifugu alboplumbeus
 * Ocellated puffer, Takifugu ocellatus
 * Obscure puffer, Takifugu obscurus
 * Finepatterned puffer, Takifugu poecilonotus

Japanese names
Incorporating new species described and other taxonomic changes since the 2013 third edition of Fishes of Japan (日本産魚類検索), edited by Nakabo Tetsuji, Motomura Hiroyuki (本村浩之) of the Kagoshima University Museum published in 2020 List of Japan's All Fish Species (日本産魚類全種目録), subtitled "Current standard Japanese and scientific names of all fish species recorded from Japanese waters"; regular open access updates are published, that of July 2021 detailing some 4,611 species.