List of mammals of Indonesia

This is a list of mammals in Indonesia. It is derived from the IUCN Red List and includes those mammals that have been extinct since 1500. The following tags are used to highlight each species' conservation status:

Order: Monotremata (monotremes)
Monotremes are mammals that lay eggs instead of giving birth to live young. Momotremata comprises the platypus and echidnas.
 * Family: Tachyglossidae (echidnas)
 * Genus: Tachyglossus
 * Short-beaked echidna, T. aculeatus
 * Genus: Zaglossus
 * Sir David's long-beaked echidna, Z. attenboroughi
 * Eastern long-beaked echidna, Z. bartoni
 * Western long-beaked echidna, Z. bruijnii

Order: Dasyuromorphia (carnivorous marsupials)
The order Dasyuromorphia comprises most of the carnivorous marsupials, including quolls, dunnarts, the numbat, the Tasmanian devil, and the recently extinct thylacine.


 * Family: Dasyuridae
 * Genus: Dasyurus
 * New Guinean quoll, D. albopunctatus
 * Bronze quoll, D. spartacus
 * Genus: Micromurexia
 * Habbema dasyure, Micromurexia habbema
 * Genus: Murexechinus
 * Black-tailed dasyure, Murexechinus melanurus
 * Genus: Murexia
 * Short-furred dasyure, Murexia longicaudata
 * Genus: Myoictis
 * Three-striped dasyure, Myoictis melas
 * Wallace's dasyure, Myoictis wallacii
 * Tate's three-striped dasyure, Myoictis wavicus
 * Genus: Neophascogale
 * Speckled dasyure,  Neophascogale lorentzi
 * Genus: Phascolosorex
 * Red-bellied marsupial shrew, Phascolosorex doriae
 * Narrow-striped marsupial shrew, Phascolosorex dorsalis
 * Genus: Phascomurexia
 * Long-nosed dasyure, Phascomurexia naso
 * Genus: Planigale
 * New Guinean planigale, Planigale novaeguineae
 * Genus: Sminthopsis
 * Chestnut dunnart, Sminthopsis archeri
 * Carpentarian dunnart, Sminthopsis butleri
 * Red-cheeked dunnart, Sminthopsis virginiae

Order: Peramelemorphia (bandicoots and bilbies)
Peramelemorphia includes the bandicoots and bilbies: it equates approximately to the mainstream of marsupial omnivores. All members of the order are endemic to the twin land masses of Australia-New Guinea and most have the characteristic bandicoot shape: a plump, arch-backed body with a long, delicately tapering snout, very large upright ears, relatively long, thin legs, and a thin tail.


 * Family: Peramelidae (bandicoots)
 * Genus: Echymipera
 * Clara's echymipera, E. clara
 * Common echymipera, E. kalubu
 * Long-nosed echymipera, E. rufescens
 * Genus: Isoodon
 * Northern brown bandicoot, I. macrourus
 * Genus: Microperoryctes
 * Arfak pygmy bandicoot, M. aplini
 * Striped bandicoot, M. longicauda
 * Mouse bandicoot, M. murina
 * Genus: Peroryctes
 * Raffray's bandicoot, P. raffrayana
 * Genus: Rhynchomeles
 * Seram bandicoot, R. prattorum

Order: Diprotodontia (kangaroos, wallabies, wombats and allies)
Diprotodontia is a large order of about 120 marsupial mammals including the kangaroos, wallabies, possums, koala, wombats, and many others. They are restricted to Australasia.
 * Family Burramyidae (pygmy possums)
 * Genus: Cercartetus
 * Long-tailed pygmy possum, Cercartetus caudatus
 * Family Phalangeridae
 * Genus: Ailurops
 * Talaud bear cuscus, Ailurops melanotis
 * Sulawesi bear cuscus, Ailurops ursinus
 * Genus: Phalanger
 * Gebe cuscus, Phalanger alexandrae
 * Mountain cuscus, Phalanger carmelitae
 * Ground cuscus, Phalanger gymnotis
 * Blue-eyed cuscus, Phalanger matabiru
 * Southern common cuscus, Phalanger mimicus
 * Northern common cuscus, Phalanger orientalis
 * Ornate cuscus, Phalanger ornatus
 * Rothschild's cuscus, Phalanger rothschildi
 * Silky cuscus, Phalanger sericeus
 * Stein's cuscus, Phalanger vestitus
 * Genus: Spilocuscus
 * Common spotted cuscus, Spilocuscus maculatus
 * Waigeou cuscus, Spilocuscus papuensis
 * Black-spotted cuscus, Spilocuscus rufoniger
 * Blue-eyed spotted cuscus, Spilocuscus wilsoni
 * Genus: Strigocuscus
 * Sulawesi dwarf cuscus, Strigocuscus celebensis
 * Banggai cuscus, Strigocuscus pelengensis
 * Family: Petauridae
 * Genus: Dactylopsila
 * Great-tailed triok, Dactylopsila megalura
 * Long-fingered triok, Dactylopsila palpator
 * Striped possum, Dactylopsila trivirgata
 * Genus: Petaurus
 * Biak glider, Petaurus biacensis
 * Krefft's glider, Petaurus notatus
 * Family: Pseudocheiridae
 * Genus: Pseudochirops
 * D'Albertis' ringtail possum, Pseudochirops albertisii
 * Plush-coated ringtail possum, Pseudochirops corinnae
 * Reclusive ringtail possum, Pseudochirops coronatus
 * Coppery ringtail possum, Pseudochirops cupreus
 * Genus: Pseudochirulus
 * Lowland ringtail possum, Pseudochirulus canescens
 * Weyland ringtail possum, Pseudochirulus caroli
 * Masked ringtail possum, Pseudochirulus larvatus
 * Pygmy ringtail possum, Pseudochirulus mayeri
 * Vogelkop ringtail possum, Pseudochirulus schlegeli
 * Family: Acrobatidae
 * Genus: Distoechurus
 * Feather-tailed possum, Distoechurus pennatus
 * Family: Macropodidae
 * Genus: Dendrolagus
 * Goodfellow's tree-kangaroo, Dendrolagus goodfellowi
 * Grizzled tree-kangaroo, Dendrolagus inustus
 * Dingiso, Dendrolagus mbaiso
 * Golden-mantled tree-kangaroo, Dendrolagus pulcherrimus
 * Seri's tree-kangaroo, Dendrolagus stellarum
 * Ursine tree-kangaroo, Dendrolagus ursinus
 * Genus: Dorcopsis
 * White-striped dorcopsis, Dorcopsis hageni
 * Gray dorcopsis, Dorcopsis luctuosa
 * Brown dorcopsis, Dorcopsis muelleri
 * Genus: Dorcopsulus
 * Small dorcopsis, Dorcopsulus vanheurni
 * Genus: Macropus
 * Agile wallaby, Macropus agilis
 * Genus: Thylogale
 * Brown's pademelon, Thylogale browni
 * Dusky pademelon, Thylogale brunii
 * Red-legged pademelon, Thylogale stigmatica

Order: Proboscidea (elephants)
The elephants comprise three living species and are the largest living land animals.
 * Family: Elephantidae
 * Genus: Elephas
 * Asian elephant, E. maximus

Order: Sirenia (manatees and dugongs)
Sirenia is an order of fully aquatic, herbivorous mammals that inhabit rivers, estuaries, coastal marine waters, swamps, and marine wetlands. All four species are endangered.
 * Family Dugongidae
 * Genus: Dugong
 * Dugong, D. dugon

Order: Scandentia (treeshrews)
The treeshrews are small mammals native to the tropical forests of Southeast Asia. Although called treeshrews, they are not true shrews and are not all arboreal.
 * Family Tupaiidae
 * Genus: Dendrogale
 * Bornean smooth-tailed treeshrew, D. melanura
 * Genus: Tupaia
 * Golden-bellied treeshrew, T. chrysogaster
 * Striped treeshrew, T. dorsalis
 * Common treeshrew, T. glis
 * Slender treeshrew, T. gracilis
 * Horsfield's treeshrew, T. javanica
 * Long-footed treeshrew, T. longipes
 * Pygmy treeshrew, T. minor
 * Painted treeshrew, T. picta
 * Ruddy treeshrew, T. splendidula
 * Large treeshrew, T. tana
 * Family Ptilocercidae
 * Genus: Ptilocercus
 * Pen-tailed treeshrew, P. lowii

Order: Dermoptera (colugos)
The two species of colugos make up the order Dermoptera. They are arboreal gliding mammals found in Southeast Asia.
 * Family Cynocephalidae
 * Genus: Galeopterus
 * Sunda flying lemur, G. variegatus

Order: Primates
The order Primates contains humans and their closest relatives: lemurs, lorisoids, monkeys, and apes.
 * Family Lorisidae
 * Genus: Nycticebus
 * Bangka slow loris, N. bancanus
 * Bornean slow loris, N. borneanus
 * Sunda slow loris, N. coucang
 * Javan slow loris, N. javanicus
 * Kayan River slow loris, N. kayan
 * Philippine slow loris, N. menagensis
 * Family Tarsiidae
 * Genus: Cephalopachus
 * Horsfield's tarsier, C. bancanus
 * Genus: Tarsius
 * Dian's tarsier, T. dentatus
 * Lariang tarsier, T. lariang
 * Peleng tarsier, T. pelengensis
 * Pygmy tarsier, T. pumilus
 * Sangihe tarsier, T. sangirensis
 * Spectral tarsier, T. tarsier
 * Family Cercopithecidae (Old World monkeys)
 * Genus: Macaca
 * Crab-eating macaque, M. fascicularis
 * Heck's macaque, M. hecki
 * Moor macaque, M. maura
 * Southern pig-tailed macaque, M. nemestrina
 * Celebes crested macaque, M. nigra
 * Gorontalo macaque, M. nigrescens
 * Booted macaque, M. ochreata
 * Pagai Island macaque, M. pagensis
 * Siberut macaque, M. siberu
 * Tonkean macaque, M. tonkeana
 * Genus: Nasalis
 * Proboscis monkey, N. larvatus
 * Genus: Presbytis
 * Black-and-white langur, P. bicolor
 * Sarawak surili, P. chrysomelas
 * Javan surili, P. comata
 * Miller's langur, P. canicrus
 * White-fronted surili, P. frontata
 * Hose's langur, P. hosei
 * Black-crested Sumatran langur, P. melalophos
 * Mitered langur, P. mitrata
 * Natuna Island surili, P. natunae
 * East Sumatran banded langur, P. percura
 * Mentawai langur, P. potenziani
 * Maroon leaf monkey, P. rubicunda
 * Saban grizzled langur, P. sabana
 * White-thighed surili, P. siamensis
 * Siberut langur, P. siberu
 * Black Sumatran langur, P. sumatrana
 * Thomas's langur, P. thomasi
 * Genus: Simias
 * Pig-tailed langur, S. concolor
 * Genus: Trachypithecus
 * East Javan langur, T. auratus
 * Silvery lutung, T. cristatus
 * West Javan langur, T. mauritius
 * Family Hylobatidae (gibbons)
 * Genus: Hylobates
 * Agile gibbon, H. agilis
 * Bornean white-bearded gibbon, H. albibarbis
 * Kloss's gibbon, H. klossii
 * Lar gibbon, H. lar
 * Silvery gibbon, H. moloch
 * Müller's gibbon, H. muelleri
 * Genus: Symphalangus
 * Siamang, S. syndactylus
 * Family Hominidae
 * Genus: Pongo
 * Sumatran orangutan, P. abelii
 * Bornean orangutan, P. pygmaeus
 * Tapanuli orangutan, P. tapanuliensis

Order: Rodentia (rodents)
Rodents make up the largest order of mammals, with over 40% of mammalian species. They have two incisors in the upper and lower jaw which grow continually and must be kept short by gnawing. Most rodents are small though the capybara can weigh up to 45 kg.
 * Family Hystricidae (Old World porcupines)
 * Genus: Atherurus
 * Asiatic brush-tailed porcupine, Atherurus macrourus
 * Genus: Hystrix
 * Malayan porcupine, H. brachyura
 * Thick-spined porcupine, Hystrix crassispinis
 * Sunda porcupine, Hystrix javanica
 * Sumatran porcupine, Hystrix sumatrae
 * Genus: Trichys
 * Long-tailed porcupine, Trichys fasciculata
 * Family Sciuridae (squirrels)
 * Genus: Aeromys
 * Black flying squirrel, Aeromys tephromelas
 * Thomas's flying squirrel, Aeromys thomasi
 * Genus: Callosciurus
 * Kloss's squirrel, Callosciurus albescens
 * Mentawai squirrel, Callosciurus melanogaster
 * Black-striped squirrel, Callosciurus nigrovittatus
 * Plantain squirrel, Callosciurus notatus
 * Borneo black-banded squirrel, Callosciurus orestes
 * Prevost's squirrel, Callosciurus prevostii
 * Genus: Dremomys
 * Bornean mountain ground squirrel, Dremomys everetti
 * Genus: Exilisciurus
 * Least pygmy squirrel, Exilisciurus exilis
 * Tufted pygmy squirrel, Exilisciurus whiteheadi
 * Genus: Hylopetes
 * Bartel's flying squirrel, Hylopetes bartelsi
 * Gray-cheeked flying squirrel, Hylopetes lepidus
 * Jentink's flying squirrel, Hylopetes platyurus
 * Sipora flying squirrel, Hylopetes sipora
 * Red-cheeked flying squirrel, Hylopetes spadiceus
 * Sumatran flying squirrel, Hylopetes winstoni
 * Genus: Hyosciurus
 * Montane long-nosed squirrel, Hyosciurus heinrichi
 * Lowland long-nosed squirrel, Hyosciurus ileile
 * Genus: Iomys
 * Javanese flying squirrel, Iomys horsfieldii
 * Mentawi flying squirrel, Iomys sipora
 * Genus: Lariscus
 * Three-striped ground squirrel, Lariscus insignis
 * Niobe ground squirrel, Lariscus niobe
 * Mentawai three-striped squirrel, Lariscus obscurus
 * Genus: Petaurista
 * Spotted giant flying squirrel, Petaurista elegans
 * Genus: Petinomys
 * Whiskered flying squirrel, Petinomys genibarbis
 * Hagen's flying squirrel, Petinomys hageni
 * Siberut flying squirrel, Petinomys lugens
 * Arrow flying squirrel, Petinomys sagitta
 * Temminck's flying squirrel, Petinomys setosus
 * Vordermann's flying squirrel, Petinomys vordermanni
 * Genus: Prosciurillus
 * Secretive dwarf squirrel, Prosciurillus abstrusus
 * Whitish dwarf squirrel, Prosciurillus leucomus
 * Celebes dwarf squirrel, Prosciurillus murinus
 * Sanghir squirrel, Prosciurillus rosenbergii
 * Weber's dwarf squirrel, Prosciurillus weberi
 * Genus: Pteromyscus
 * Smoky flying squirrel, Pteromyscus pulverulentus
 * Genus: Ratufa
 * Cream-coloured giant squirrel, Ratufa affinis
 * Black giant squirrel, Ratufa bicolor
 * Genus: Rheithrosciurus
 * Tufted ground squirrel, Rheithrosciurus macrotis
 * Genus: Rhinosciurus
 * Shrew-faced squirrel, Rhinosciurus laticaudatus
 * Genus: Rubrisciurus
 * Red-bellied squirrel, Rubrisciurus rubriventer
 * Genus: Sundasciurus
 * Brooke's squirrel, Sundasciurus brookei
 * Fraternal squirrel, Sundasciurus fraterculus
 * Horse-tailed squirrel, Sundasciurus hippurus
 * Jentink's squirrel, Sundasciurus jentinki
 * Low's squirrel, Sundasciurus lowii
 * Slender squirrel, Sundasciurus tenuis
 * Family Spalacidae
 * Genus: Rhizomys
 * Large bamboo rat, Rhizomys sumatrensis
 * Family Muridae
 * Genus: Anisomys
 * Squirrel-toothed rat, Anisomys imitator
 * Genus: Baiyankamys
 * Mountain water rat, Baiyankamys habbema
 * Genus: Bandicota
 * Lesser bandicoot rat, Bandicota bengalensis
 * Greater bandicoot rat, Bandicota indica
 * Genus: Berylmys
 * Bower's white-toothed rat, Berylmys bowersi
 * Genus: Bunomys
 * Andrew's hill rat, Bunomys andrewsi
 * Yellow-haired hill rat, Bunomys chrysocomus
 * Heavenly hill rat, Bunomys coelestis
 * Fraternal hill rat, Bunomys fratrorum
 * Inland hill rat, Bunomys penitus
 * Long-headed hill rat, Bunomys prolatus
 * Genus: Chiropodomys
 * Indomalayan pencil-tailed tree mouse, Chiropodomys gliroides
 * Koopman's pencil-tailed tree mouse, Chiropodomys karlkoopmani
 * Gray-bellied pencil-tailed tree mouse, Chiropodomys muroides
 * Small pencil-tailed tree mouse, Chiropodomys pusillus
 * Genus: Coccymys
 * White-toothed brush mouse, Coccymys albidens
 * Rümmler's brush mouse, Coccymys ruemmleri
 * Genus: Coryphomys
 * Buhler's coryphomys, Coryphomys buehleri
 * Genus: Echiothrix
 * Central Sulawesi echiothrix, Echiothrix centrosa
 * Northern Sulawesi echiothrix, Echiothrix leucura
 * Genus: Eropeplus
 * Sulawesi soft-furred rat, Eropeplus canus
 * Genus: Haeromys
 * Ranee mouse, Haeromys margarettae
 * Minahassa ranee mouse, Haeromys minahassae
 * Lesser ranee mouse, Haeromys pusillus
 * Genus: Hydromys
 * Rakali, Hydromys chrysogaster
 * Western water rat, Hydromys hussoni
 * Genus: Hyomys
 * Western white-eared giant rat, Hyomys dammermani
 * Genus: Kadarsanomys
 * Sody's tree rat, Kadarsanomys sodyi
 * Genus: Komodomys
 * Komodo rat, Komodomys rintjanus
 * Genus: Lenomys
 * Trefoil-toothed giant rat, Lenomys meyeri
 * Genus: Lenothrix
 * Gray tree rat, Lenothrix canus
 * Genus: Leopoldamys
 * Sundaic mountain leopoldamys, Leopoldamys ciliatus
 * Diwangkara's long-tailed giant rat, Leopoldamys diwangkarai
 * Long-tailed giant rat, Leopoldamys sabanus
 * Mentawai long-tailed giant rat, Leopoldamys siporanus
 * Genus: Lorentzimys
 * New Guinean jumping mouse, Lorentzimys nouhuysi
 * Genus: Mallomys
 * De Vis's woolly rat, Mallomys aroaensis
 * Alpine woolly rat, Mallomys gunung
 * Subalpine woolly rat, Mallomys istapantap
 * Rothschild's woolly rat, Mallomys rothschildi
 * Genus: Mammelomys
 * Large-scaled mosaic-tailed rat, Mammelomys lanosus
 * Large mosaic-tailed rat, Mammelomys rattoides
 * Genus: Margaretamys
 * Beccari's margareta rat, Margaretamys beccarii
 * Elegant margareta rat, Margaretamys elegans
 * Little margareta rat, Margaretamys parvus
 * Christine's margareta rat, Margaretamys christinae
 * Genus: Maxomys
 * Bartels's spiny rat, Maxomys bartelsii
 * Dollman's spiny rat, Maxomys dollmani
 * Hellwald's spiny rat, Maxomys hellwaldii
 * Sumatran spiny rat, Maxomys hylomyoides
 * Musschenbroek's spiny rat, Maxomys musschenbroekii
 * Fat-nosed spiny rat, Maxomys inflatus
 * Chestnut-bellied spiny rat, Maxomys ochraceiventer
 * Pagai spiny rat, Maxomys pagensis
 * Rajah spiny rat, Maxomys rajah
 * Red spiny rat, Maxomys surifer
 * Watts's spiny rat, Maxomys wattsi
 * Whitehead's spiny rat, Maxomys whiteheadi
 * Genus: Melasmothrix
 * Sulawesian shrew rat, Melasmothrix naso
 * Genus: Melomys
 * Dusky mosaic-tailed rat, Melomys aerosus
 * Bannister's rat, Melomys bannisteri
 * Yamdena mosaic-tailed rat, Melomys cooperae
 * Manusela mosaic-tailed rat, Melomys fraterculus
 * Snow Mountains grassland mosaic-tailed rat, Melomys frigicola
 * Seram long-tailed mosaic-tailed rat, Melomys fulgens
 * Riama mosaic-tailed rat, Melomys howi
 * White-bellied mosaic-tailed rat, Melomys leucogaster
 * Papua grassland mosaic-tailed rat, Melomys lutillus
 * Obi mosaic-tailed rat, Melomys obiensis
 * Pavel's Seram mosaic-tailed rat, Melomys paveli
 * Black-tailed mosaic-tailed rat, Melomys rufescens
 * Short-tailed Talaud mosaic-tailed rat, Melomys caurinus
 * Long-tailed Talaud mosaic-tailed rat, Melomys talaudium
 * Genus: Microhydromys
 * Northern groove-toothed shrew mouse, Microhydromys richardsoni
 * Genus: Mus
 * Ryukyu mouse, Mus caroli
 * Fawn-colored mouse, Mus cervicolor
 * Sumatran shrewlike mouse, Mus crociduroides
 * House mouse, M. musculus
 * Earth-colored mouse, Mus terricolor
 * Volcano mouse, Mus vulcani
 * Genus: Nesoromys
 * Ceram rat, Nesoromys ceramicus
 * Genus: Niviventer
 * Dark-tailed tree rat, Niviventer cremoriventer
 * Montane Sumatran white-bellied rat, Niviventer fraternus
 * Chestnut white-bellied rat, Niviventer fulvescens
 * Narrow-tailed white-bellied rat, Niviventer lepturus
 * Long-tailed mountain rat, Niviventer rapit
 * Genus: Papagomys
 * Flores giant rat, Papagomys armandvillei
 * Verhoeven's giant tree rat, Papagomys theodorverhoeveni
 * Genus: Parahydromys
 * New Guinea waterside rat, Parahydromys asper
 * Genus: Paraleptomys, 
 * Northern water rat, Paraleptomys rufilatus
 * Short-haired water rat, Paraleptomys wilhelmina
 * Genus: Paramelomys
 * Lorentz's mosaic-tailed rat, Paramelomys lorentzii
 * Thomas's mosaic-tailed rat, Paramelomys mollis
 * Long-nosed paramelomys, Paramelomys naso
 * Lowland mosaic-tailed rat, Paramelomys platyops
 * Mountain mosaic-tailed rat, Paramelomys rubex
 * Stein's paramelomys, Paramelomys steini
 * Genus: Paruromys
 * Sulawesi giant rat, Paruromys dominator
 * Genus: Paulamys
 * Flores long-nosed rat, Paulamys naso
 * Genus: Pithecheir
 * Red tree rat, Pithecheir melanurus
 * Genus: Pithecheirops
 * Bornean pithecheirops, Pithecheirops otion
 * Genus: Pogonomelomys
 * Grey pogonomelomys, Pogonomelomys brassi
 * Lowland brush mouse, Pogonomelomys bruijni
 * Shaw Mayer's brush mouse, Pogonomelomys mayeri
 * Genus: Pogonomys
 * Large tree mouse, Pogonomys loriae
 * Chestnut tree mouse, Pogonomys macrourus
 * Gray-bellied tree mouse, Pogonomys sylvestris
 * Genus: Pseudohydromys
 * One-toothed shrew mouse, Pseudohydromys ellermani
 * Western shrew mouse, Pseudohydromys occidentalis
 * Genus: Rattus
 * Sunburned rat, Rattus adustus
 * Annandale's rat, Rattus annandalei
 * Vogelkop mountain rat, Rattus arfakiensis
 * Ricefield rat, Rattus argentiventer
 * Western New Guinea mountain rat, Rattus arrogans
 * Aceh rat, Rattus blangorum
 * Bonthain rat, Rattus bontanus
 * Sula rat, Rattus elaphinus
 * Enggano rat, Rattus enganus
 * Polynesian rat, Rattus exulans
 * Spiny Ceram rat, Rattus feliceus
 * Hainald's rat, Rattus hainaldi
 * Hoffmann's rat, Rattus hoffmanni
 * Hoogerwerf's rat, Rattus hoogerwerfi
 * Japen rat, Rattus jobiensis
 * Koopman's rat, Rattus koopmani
 * Korinch's rat, Rattus korinchi
 * Mentawai rat, Rattus lugens
 * Opossum rat, Rattus marmosurus
 * Little soft-furred rat, Rattus mollicomulus
 * Molaccan prehensile-tailed rat, Rattus morotaiensis
 * Himalayan field rat, Rattus nitidus
 * Brown rat, R. norvegicus introduced
 * Arianus's rat, Rattus omichlodes
 * Peleng rat, Rattus pelurus
 * Large New Guinea spiny rat, Rattus praetor
 * Black rat, Rattus rattus
 * Glacier rat, Rattus richardsoni
 * Southeastern xanthurus rat, Rattus salocco
 * Simalur rat, Rattus simalurensis
 * Stein's rat, Rattus steini
 * Tanezumi rat, Rattus tanezumi
 * Timor rat, Rattus timorensis
 * Malayan field rat, Rattus tiomanicus
 * Slender rat, Rattus verecundus
 * Yellow-tailed rat, Rattus xanthurus
 * Genus: Sommeromys
 * Sommer's Sulawesi rat, Sommeromys macrorhinos
 * Genus: Spelaeomys
 * Flores cave rat, Spelaeomys florensis
 * Genus: Sundamys
 * Mountain giant Sunda rat, Sundamys infraluteus
 * Bartels's rat, Sundamys maxi
 * Müller's giant Sunda rat, Sundamys muelleri
 * Genus: Taeromys
 * Salokko rat, Taeromys arcuatus
 * Lovely-haired rat, Taeromys callitrichus
 * Celebes rat, Taeromys celebensis
 * Sulawesi montane rat, Taeromys hamatus
 * Small-eared rat, Taeromys microbullatus
 * Sulawesi forest rat, Taeromys punicans
 * Tondano rat, Taeromys taerae
 * Genus: Tateomys
 * Long-tailed shrew rat, Tateomys macrocercus
 * Tate's shrew rat, Tateomys rhinogradoides
 * Genus: Uromys
 * Giant naked-tailed rat, Uromys anak
 * Biak giant rat, Uromys boeadii
 * Giant white-tailed rat, Uromys caudimaculatus
 * Emma's giant rat, Uromys emmae
 * Great Key Island giant rat, Uromys siebersi
 * Genus: Xenuromys
 * Mimic tree rat, Xenuromys barbatus

Order: Lagomorpha (lagomorphs)
The lagomorphs comprise two families, Leporidae (hares and rabbits), and Ochotonidae (pikas). Though they can resemble rodents, and were classified as a superfamily in that order until the early 20th century, they have since been considered a separate order. They differ from rodents in a number of physical characteristics, such as having four incisors in the upper jaw rather than two.
 * Family Leporidae
 * Genus: Lepus
 * Indian hare, L. nigricollis possibly introduced
 * Genus: Nesolagus
 * Sumatran striped rabbit, Nesolagus netscheri

Order Eulipotyphla (shrews, moles, and hedgehogs)
The "shrew-forms" are insectivorous mammals. The shrews and solenodons closely resemble mice while the moles are stout-bodied burrowers. The hedgehogs are easily recognised by their spines while gymnures look more like large rats.
 * Family: Erinaceidae
 * Genus: Echinosorex
 * Moonrat, Echinosorex gymnura
 * Genus: Hylomys
 * Dwarf gymnure, Hylomys parvus
 * Bornean short-tailed gymnure, Hylomys dorsalis
 * Max's short-tailed gymnure, Hylomys maxi
 * Javan short-tailed gymnure, Hylomys suillus
 * Leuser short-tailed gymnure, Hylomys vorax
 * Family: Soricidae (shrews)
 * Genus: Chimarrogale
 * Bornean water shrew, Chimarrogale phaeura
 * Sumatran water shrew, Chimarrogale sumatrana
 * Genus: Crocidura
 * Kinabalu shrew, Crocidura baluensis
 * Batak shrew, Crocidura batakorum
 * Beccari's shrew, Crocidura beccarii
 * Thick-tailed shrew, Crocidura brunnea
 * Elongated shrew, Crocidura elongata
 * Bornean shrew, Crocidura foetida
 * Hill's shrew, Crocidura hilliana
 * Hutan shrew, Crocidura hutanis
 * Jenkins' shrew, Crocidura jenkinsi
 * Sulawesi shrew, Crocidura lea
 * Sumatran giant shrew, Crocidura lepidura
 * Sulawesi tiny shrew, Crocidura levicula
 * Malayan shrew, Crocidura malayana
 * Javanese shrew, Crocidura maxi
 * Sunda shrew, Crocidura monticola
 * Mossy forest shrew, Crocidura musseri
 * Peninsular shrew, Crocidura negligens
 * Black-footed shrew, Crocidura nigripes
 * Oriental shrew, Crocidura orientalis
 * Sumatran long-tailed shrew, Crocidura paradoxura
 * Sulawesi white-handed shrew, Crocidura rhoditis
 * Timor shrew, Crocidura tenuis
 * Banka shrew, Crocidura vosmaeri
 * Genus: Suncus
 * Flores shrew, Suncus mertensi
 * Asian house shrew, S. murinus

Order: Chiroptera (bats)
The bats' most distinguishing feature is that their forelimbs are developed as wings, making them the only mammals capable of flight. Bat species account for about 20% of all mammals.
 * Family: Pteropodidae (megabats)
 * Genus: Acerodon
 * Sulawesi flying fox, Acerodon celebensis
 * Talaud flying fox, Acerodon humilis
 * Sunda flying fox, Acerodon mackloti
 * Genus: Aethalops
 * Borneo fruit bat, Aethalops aequalis
 * Pygmy fruit bat, Aethalops alecto
 * Genus: Aproteles
 * Bulmer's fruit bat, Aproteles bulmerae
 * Genus: Balionycteris
 * Spotted-winged fruit bat, Balionycteris maculata
 * Genus: Chironax
 * Black-capped fruit bat, Chironax melanocephalus
 * Genus: Cynopterus
 * Lesser short-nosed fruit bat, C. brachyotis
 * Horsfield's fruit bat, Cynopterus horsfieldi
 * Peters's fruit bat, Cynopterus luzoniensis
 * Minute fruit bat, Cynopterus minutus
 * Nusatenggara short-nosed fruit bat, Cynopterus nusatenggara
 * Greater short-nosed fruit bat, Cynopterus sphinx
 * Indonesian short-nosed fruit bat, Cynopterus titthaecheileus
 * Genus: Dobsonia
 * Beaufort's naked-backed fruit bat, Dobsonia beauforti
 * Halmahera naked-backed fruit bat, Dobsonia crenulata
 * Biak naked-backed fruit bat, Dobsonia emersa
 * Sulawesi naked-backed fruit bat, Dobsonia exoleta
 * Lesser naked-backed fruit bat, Dobsonia minor
 * Moluccan naked-backed fruit bat, Dobsonia moluccensis
 * Western naked-backed fruit bat, Dobsonia peronii
 * Greenish naked-backed fruit bat, Dobsonia viridis
 * Genus: Dyacopterus
 * Brooks's dyak fruit bat, Dyacopterus brooksi
 * Dayak fruit bat, Dyacopterus spadiceus
 * Genus: Eonycteris
 * Greater nectar bat, Eonycteris major
 * Cave nectar bat, Eonycteris spelaea
 * Genus: Harpyionycteris
 * Sulawesi harpy fruit bat, Harpyionycteris celebensis
 * Genus: Macroglossus
 * Long-tongued nectar bat, Macroglossus minimus
 * Long-tongued fruit bat, Macroglossus sobrinus
 * Genus: Megaerops
 * Tailless fruit bat, Megaerops ecaudatus
 * Javan tailless fruit bat, Megaerops kusnotoi
 * White-collared fruit bat, Megaerops wetmorei
 * Genus: Neopteryx
 * Small-toothed fruit bat, Neopteryx frosti
 * Genus: Nyctimene
 * Broad-striped tube-nosed fruit bat, Nyctimene aello
 * Common tube-nosed fruit bat, Nyctimene albiventer
 * Pallas's tube-nosed bat, Nyctimene cephalotes
 * Mountain tube-nosed fruit bat, Nyctimene certans
 * Round-eared tube-nosed fruit bat, Nyctimene cyclotis
 * Dragon tube-nosed fruit bat, Nyctimene draconilla
 * Keast's tube-nosed fruit bat, Nyctimene keasti
 * Lesser tube-nosed bat, Nyctimene minutus
 * Genus: Paranyctimene
 * Lesser tube-nosed fruit bat, Paranyctimene raptor
 * Steadfast tube-nosed fruit bat, Paranyctimene tenax
 * Genus: Penthetor
 * Dusky fruit bat, Penthetor lucasi
 * Genus: Pteropus
 * Black flying fox, Pteropus alecto
 * Aru flying fox, Pteropus aruensis
 * Ashy-headed flying fox, Pteropus caniceps
 * Moluccan flying fox, Pteropus chrysoproctus
 * Spectacled flying fox, Pteropus conspicillatus
 * Gray flying fox, Pteropus griseus
 * Small flying fox, Pteropus hypomelanus
 * Kei flying fox, Pteropus keyensis
 * Lombok flying fox, Pteropus lombocensis
 * Big-eared flying fox, Pteropus macrotis
 * Black-bearded flying fox, Pteropus melanopogon
 * Black-eared flying fox, Pteropus melanotus
 * Great flying fox, Pteropus neohibernicus
 * Ceram fruit bat, Pteropus ocularis
 * Masked flying fox, Pteropus personatus
 * Geelvink Bay flying fox, Pteropus pohlei
 * Philippine gray flying fox, Pteropus speciosus
 * Temminck's flying fox, Pteropus temmincki
 * Large flying fox, Pteropus vampyrus
 * Genus: Rousettus
 * Geoffroy's rousette, Rousettus amplexicaudatus
 * Manado fruit bat, Rousettus bidens
 * Sulawesi rousette, Rousettus celebensis
 * Leschenault's rousette, Rousettus leschenaulti
 * Linduan rousette, Rousettus linduensis
 * Bare-backed rousette, Rousettus spinalatus
 * Genus: Styloctenium
 * Sulawesi stripe-faced fruit batStyloctenium wallacei
 * Genus: Syconycteris
 * Common blossom bat, Syconycteris australis
 * Halmahera blossom bat, Syconycteris carolinae
 * Moss-forest blossom bat, Syconycteris hobbit
 * Genus: Thoopterus
 * Swift fruit bat, Thoopterus nigrescens
 * Family Rhinopomatidae
 * Genus: Rhinopoma
 * Greater mouse-tailed bat, Rhinopoma microphyllum
 * Family Megadermatidae (false vampire bats)
 * Genus: Megaderma
 * Lesser false vampire bat, Megaderma spasma
 * Family Rhinolophidae (horseshoe bats)
 * Genus: Rhinolophus
 * Acuminate horseshoe bat, Rhinolophus acuminatus
 * Intermediate horseshoe bat, Rhinolophus affinis
 * Arcuate horseshoe bat, Rhinolophus arcuatus
 * Bornean horseshoe bat, Rhinolophus borneensis
 * Canut's horseshoe bat, Rhinolophus canuti
 * Sulawesi horseshoe bat, Rhinolophus celebensis
 * Creagh's horseshoe bat, Rhinolophus creaghi
 * Broad-eared horseshoe bat, Rhinolophus euryotis
 * Insular horseshoe bat, Rhinolophus keyensis
 * Blyth's horseshoe bat, Rhinolophus lepidus
 * Woolly horseshoe bat, Rhinolophus luctus
 * Big-eared horseshoe bat, Rhinolophus macrotis
 * Madura horseshoe bat, Rhinolophus madurensis
 * Smaller horseshoe bat, Rhinolophus megaphyllus
 * Neriad horseshoe bat, Rhinolophus nereis NT
 * Large-eared horseshoe bat, Rhinolophus philippinensis NT
 * Least horseshoe bat, Rhinolophus pusillus LC
 * Lesser woolly horseshoe bat, Rhinolophus sedulus
 * Lesser brown horseshoe bat, Rhinolophus stheno LC
 * Trefoil horseshoe bat, Rhinolophus trifoliatus LC
 * Family Hipposideridae
 * Genus: Aselliscus
 * Temminck's trident bat, Aselliscus tricuspidatus LC
 * Genus: Coelops
 * East Asian tailless leaf-nosed bat, Coelops frithii LC
 * Malayan tailless leaf-nosed bat, Coelops robinsoni VU
 * Genus: Hipposideros
 * Dusky roundleaf bat, Hipposideros ater LC
 * Bicolored roundleaf bat, Hipposideros bicolor LC
 * Short-headed roundleaf bat, Hipposideros breviceps VU
 * Spurred roundleaf bat, Hipposideros calcaratus LC
 * Fawn leaf-nosed bat, Hipposideros cervinus LC
 * Ashy roundleaf bat, Hipposideros cineraceus LC
 * Telefomin roundleaf bat, Hipposideros corynophyllus VU
 * Timor roundleaf bat, Hipposideros crumeniferus DD
 * Diadem leaf-nosed bat, Hipposideros diadema LC
 * Borneo roundleaf bat, Hipposideros doriae NT
 * Dayak roundleaf bat, Hipposideros dyacorum LC
 * Cantor's roundleaf bat, Hipposideros galeritus LC
 * Crested roundleaf bat, Hipposideros inexpectatus
 * Intermediate roundleaf bat, Hipposideros larvatus LC
 * Big-eared roundleaf bat, Hipposideros macrobullatus
 * Maduran leaf-nosed bat, Hipposideros madurae
 * Maggie Taylor's roundleaf bat, Hipposideros maggietaylorae
 * Fly River roundleaf bat, Hipposideros muscinus
 * Orbiculus leaf-nosed bat, Hipposideros orbiculus
 * Biak roundleaf bat, Hipposideros papua
 * Peleng leaf-nosed bat, Hipposideros pelingensis
 * Sorensen's leaf-nosed bat, Hipposideros sorenseni
 * Sumba roundleaf bat, Hipposideros sumbae
 * Wollaston's roundleaf bat, Hipposideros wollastoni
 * Family Emballonuridae (sac-winged bats)
 * Genus: Emballonura
 * Small Asian sheath-tailed bat, Emballonura alecto
 * Beccari's sheath-tailed bat, Emballonura beccarii
 * Greater sheath-tailed bat, Emballonura furax
 * Lesser sheath-tailed bat, Emballonura monticola
 * Raffray's sheath-tailed bat, Emballonura raffrayana
 * Genus: Mosia
 * Dark sheath-tailed bat, Mosia nigrescens
 * Genus: Saccolaimus
 * Naked-rumped pouched bat, Saccolaimus saccolaimus
 * Genus: Taphozous
 * Indonesian tomb bat, Taphozous achates
 * Long-winged tomb bat, Taphozous longimanus
 * Black-bearded tomb bat, Taphozous melanopogon
 * Theobald's tomb bat, Taphozous theobaldi
 * Family: Nycteridae (slit-faced bats)
 * Genus: Nycteris
 * Javan slit-faced bat, Nycteris javanica
 * Malayan slit-faced bat, Nycteris tragata
 * Family: Molossidae (free-tailed bats)
 * Genus: Chaerephon
 * Northern freetail bat, Chaerephon jobensis
 * Northern free-tailed bat, Chaerephon johorensis
 * Genus: Cheiromeles
 * Lesser naked bat, Cheiromeles parvidens
 * Hairless bat, Cheiromeles torquatus
 * Genus: Mops
 * Malayan free-tailed bat, Mops mops
 * Sulawesi free-tailed bat, Mops sarasinorum
 * Genus: Mormopterus
 * Beccari's free-tailed bat, Mormopterus beccarii
 * Sumatran mastiff bat, Mormopterus doriae
 * Genus: Otomops
 * Javan mastiff bat, Otomops formosus
 * Johnstone's mastiff bat, Otomops johnstonei
 * Family Vespertilionidae (vesper bats)
 * Genus: Arielulus
 * Black-gilded pipistrelle, Arielulus circumdatus
 * Coppery pipistrelle, Arielulus cuprosus
 * Genus: Falsistrellus
 * Pungent pipistrelle, Falsistrellus mordax
 * Peters's pipistrelle, Falsistrellus petersi
 * Genus: Glischropus
 * Javan thick-thumbed bat, Glischropus javanus
 * Common thick-thumbed bat, Glischropus tylopus
 * Genus: Harpiocephalus
 * Lesser hairy-winged bat, Harpiocephalus harpia
 * Greater hairy-winged bat, Harpiocephalus mordax
 * Genus: Hesperoptenus
 * Blanford's bat, Hesperoptenus blanfordi
 * False serotine bat, Hesperoptenus doriae
 * Gaskell's false serotine, Hesperoptenus gaskelli
 * Large false serotine, Hesperoptenus tomesi
 * Genus: Hypsugo
 * Brown pipistrelle, Hypsugo imbricatus
 * Red-brown pipistrelle, Hypsugo kitcheneri
 * Big-eared pipistrelle, Hypsugo macrotis
 * Vordermann's pipistrelle, Hypsugo vordermanni
 * Genus: Kerivoula
 * Flores woolly bat, Kerivoula flora
 * Hardwicke's woolly bat, Kerivoula hardwickii
 * Small woolly bat, Kerivoula intermedia
 * Papillose woolly bat, Kerivoula papillosa
 * Clear-winged woolly bat, Kerivoula pellucida
 * Painted bat, Kerivoula picta
 * Whitehead's woolly bat, Kerivoula whiteheadi
 * Genus: Miniopterus
 * Little bent-wing bat, Miniopterus australis
 * Miniopterus macrocneme
 * Western bent-winged bat, Miniopterus magnater
 * Intermediate long-fingered bat, Miniopterus medius
 * Philippine long-fingered bat, Miniopterus paululus
 * Small bent-winged bat, Miniopterus pusillus
 * Common bent-wing bat, M. schreibersii
 * Shortridges's long-fingered bat, Miniopterus shortridgei
 * Great bent-winged bat, Miniopterus tristis
 * Genus: Murina
 * Bronze tube-nosed bat, Murina aenea
 * Round-eared tube-nosed bat, Murina cyclotis
 * Flute-nosed bat, Murina florium
 * Gilded tube-nosed bat, Murina rozendaali
 * Brown tube-nosed bat, Murina suilla
 * Genus: Myotis
 * Large-footed bat, Myotis adversus
 * Peters's myotis, Myotis ater
 * Hodgson's bat, M. formosus
 * Lesser large-footed bat, Myotis hasseltii
 * Herman's myotis, Myotis hermani
 * Horsfield's bat, Myotis horsfieldii
 * Pallid large-footed myotis, Myotis macrotarsus
 * Maluku myotis, Myotis moluccarum
 * Burmese whiskered bat, Myotis montivagus
 * Wall-roosting mouse-eared bat, Myotis muricola
 * Ridley's bat, Myotis ridleyi
 * Himalayan whiskered bat, Myotis siligorensis
 * Kei myotis, Myotis stalkeri
 * Genus: Nyctophilus
 * Sunda long-eared bat, Nyctophilus heran
 * Greater long-eared bat, Nyctophilus timoriensis
 * Genus: Philetor
 * Rohu's bat, Philetor brachypterus
 * Genus: Phoniscus
 * Groove-toothed bat, Phoniscus atrox
 * Peters's trumpet-eared bat, Phoniscus jagorii
 * Golden-tipped bat, Phoniscus papuensis
 * Genus: Pipistrellus
 * Angulate pipistrelle, Pipistrellus angulatus
 * Kelaart's pipistrelle, Pipistrellus ceylonicus
 * Java pipistrelle, Pipistrellus javanicus
 * Minahassa pipistrelle, Pipistrellus minahassae
 * Lesser Papuan pipistrelle, Pipistrellus papuanus
 * Narrow-winged pipistrelle, Pipistrellus stenopterus
 * Least pipistrelle, Pipistrellus tenuis
 * Genus: Scotophilus
 * Sulawesi yellow bat, Scotophilus celebensis
 * Sody's yellow house bat, Scotophilus collinus
 * Lesser Asiatic yellow bat, Scotophilus kuhlii
 * Genus: Scotorepens
 * Northern broad-nosed bat, Scotorepens sanborni
 * Genus: Tylonycteris
 * Lesser bamboo bat, Tylonycteris pachypus
 * Greater bamboo bat, Tylonycteris robustula

Order Pholidota (pangolins)
The order Pholidota comprises the eight species of pangolin. Pangolins are anteaters and have the powerful claws, elongated snout and long tongue seen in the other unrelated anteater species.
 * Family Manidae
 * Genus: Manis
 * Sunda pangolin, M. javanica

Order: Cetacea (whales)
The order Cetacea includes whales, dolphins and porpoises. They are the mammals most fully adapted to aquatic life with a spindle-shaped nearly hairless body, protected by a thick layer of blubber, and forelimbs and tail modified to provide propulsion underwater.
 * Family: Balaenopteridae (rorquals)
 * Genus: Balaenoptera
 * Common minke whale, Balaenoptera acutorostrata
 * Antarctic minke whale, Balaenoptera bonaerensis
 * Sei whale, Balaenoptera borealis
 * Bryde's whale, Balaenoptera brydei
 * Blue whale, Balaenoptera musculus
 * Fin whale, Balaenoptera physalus
 * Omura's whale, Balaenoptera omurai
 * Genus: Megaptera
 * Humpback whale, Megaptera novaeangliae
 * Family Physeteridae (sperm whales)
 * Genus: Physeter
 * Sperm whale, Physeter macrocephalus
 * Family: Kogiidae (small sperm whales)
 * Genus: Kogia
 * Pygmy sperm whale, K. breviceps
 * Dwarf sperm whale, Kogia sima
 * Family: Phocoenidae (porpoises)
 * Genus: Neophocaena
 * Indo-Pacific finless porpoise, Neophocaena phocaenoides
 * Family Ziphiidae (beaked whales)
 * Genus: Mesoplodon
 * Blainville's beaked whale, Mesoplodon densirostris
 * Ginkgo-toothed beaked whale, Mesoplodon ginkgodens
 * Genus: Ziphius
 * Cuvier's beaked whaleZiphius cavirostris
 * Family: Delphinidae (oceanic dolphins)
 * Genus: Delphinus
 * Common dolphin, Delphinus delphis
 * Genus: Feresa
 * Pygmy killer whale, Feresa attenuata
 * Genus: Globicephala
 * Short-finned pilot whale, Globicephala macrorhynchus
 * Genus: Grampus
 * Risso's dolphin, Grampus griseus
 * Genus: Lagenodelphis
 * Fraser's dolphin, Lagenodelphis hosei
 * Genus: Orcaella
 * Irrawaddy dolphin, O. brevirostris
 * Australian snubfin dolphin, Orcaella heinsohni
 * Genus: Orcinus
 * Orca, O. orca
 * Genus: Peponocephala
 * Melon-headed whale, Peponocephala electra
 * Genus: Pseudorca
 * False killer whale, Pseudorca crassidens
 * Genus: Sousa
 * Indo-Pacific humpback dolphin, Sousa chinensis
 * Genus: Stenella
 * Pantropical spotted dolphin, Stenella attenuata
 * Striped dolphin, Stenella coeruleoalba
 * Spinner dolphin, Stenella longirostris
 * Genus: Steno
 * Rough-toothed dolphin, Steno bredanensis
 * Genus: Tursiops
 * Indo-Pacific bottlenose dolphin, Tursiops aduncus
 * Common bottlenose dolphin, Tursiops truncatus

Order: Carnivora (carnivorans)
There are over 260 species of carnivorans, the majority of which feed primarily on meat. They have a characteristic skull shape and dentition.
 * Family Felidae (cats)
 * Genus: Catopuma
 * Bay cat, C. badia
 * Asian golden cat, C. temminckii
 * Genus: Neofelis
 * Sunda clouded leopard, N. diardi
 * Genus: Panthera
 * Leopard, P. pardus
 * Javan leopard, P. p. melas
 * Tiger, P. tigris
 * Bali tiger, P. t. sondaica
 * Javan tiger, P. t. sondaica
 * Sumatran tiger, P. t. sondaica
 * Genus: Pardofelis
 * Marbled cat, P. marmorata
 * Genus: Prionailurus
 * Sunda leopard cat, P. javanensis
 * Flat-headed cat, P. planiceps
 * Fishing cat, P. viverrinus presence uncertain
 * Family Viverridae (civets)
 * Genus: Arctictis
 * Binturong, A. binturong
 * Genus: Arctogalidia
 * Small-toothed palm civet, A. trivirgata
 * Genus: Cynogale
 * Otter civet, C. bennettii
 * Genus: Hemigalus
 * Banded palm civet, H. derbyanus
 * Genus: Macrogalidia
 * Sulawesi palm civet, M. musschenbroekii
 * Genus: Paguma
 * Masked palm civet, P. larvata
 * Genus: Paradoxurus
 * Asian palm civet, P. hermaphroditus
 * Genus: Viverra
 * Malayan civet, V. tangalunga
 * Genus: Viverricula
 * Small Indian civet, V. indica
 * Family Prionodontidae (linsangs)
 * Genus: Prionodon
 * Banded linsang, P. linsang
 * Family Herpestidae (mongooses)
 * Genus: Urva
 * Short-tailed mongoose, U. brachyura
 * Javan mongoose, U. javanica
 * Collared mongoose, U. semitorquata
 * Family Ursidae (bears)
 * Genus: Helarctos
 * Sun bear, H. malayanus
 * Family Canidae (Canids)
 * Genus: Cuon
 * Dhole, C. alpinus
 * Family: Mustelidae (weasels)
 * Genus: Aonyx
 * Asian small-clawed otter, A. cinereus
 * Genus: Arctonyx
 * Sumatran hog badger, A. hoevenii
 * Genus: Lutra
 * Eurasian otter, L. lutra
 * Hairy-nosed otter, L. sumatrana
 * Genus: Lutrogale
 * Smooth-coated otter, L. perspicillata
 * Genus: Martes
 * Yellow-throated marten, M. flavigula
 * Genus: Melogale
 * Bornean ferret-badger, M. everetti
 * Javan ferret-badger, M. orientalis
 * Genus: Mustela
 * Indonesian mountain weasel, M. lutreolina
 * Malayan weasel, M. nudipes
 * Family Mephitidae (skunks)
 * Genus: Mydaus
 * Sunda stink badger, M. javanensis

Order: Perissodactyla (odd-toed ungulates)
The odd-toed ungulates are browsing and grazing mammals. They are usually large to very large, and have relatively simple stomachs and a large middle toe.
 * Family Rhinocerotidae (rhinoceroses)
 * Genus: Dicerorhinus
 * Sumatran rhinoceros, D. sumatrensis
 * Genus: Rhinoceros
 * Javan rhinoceros, R. sondaicus
 * Family Tapiridae (tapirs)
 * Genus: Acrocodia
 * Malayan tapir, A. indicus

Order: Artiodactyla (even-toed ungulates)
The even-toed ungulates are ungulates whose weight is borne about equally by the third and fourth toes, rather than mostly or entirely by the third as in perissodactyls. There are about 220 artiodactyl species, including many that are of great economic importance to humans.
 * Family Suidae (pigs)
 * Genus: Babyrousa
 * Buru babirusa, B. babyrussa
 * Bola Batu babirusa, B. bolabatuensis
 * North Sulawesi babirusa, B. celebensis
 * Togian babirusa, B. togeanensis
 * Genus: Sus
 * Bornean bearded pig, S. barbatus
 * Celebes warty pig, S. celebensis
 * Wild boar, S. scrofa
 * Javan warty pig, S. verrucosus
 * Family Tragulidae (mouse deer)
 * Genus: Tragulus
 * Java mouse-deer, T. javanicus
 * Lesser mouse-deer, T. kanchil
 * Greater mouse-deer, T. napu
 * Family Bovidae (Bovids)
 * Genus: Bos
 * Banteng, B. javanicus
 * Genus: Bubalus
 * Lowland anoa, B. depressicornis
 * Mountain anoa, B. quarlesi
 * Genus: Capricornis
 * Mainland serow, C. sumatraensis
 * Family Cervidae (deer)
 * Genus: Axis
 * Bawean deer, A. kuhlii
 * Genus: Muntiacus
 * Bornean yellow muntjac, M. atherodes
 * Sumatran muntjac, M. montanus
 * Indian muntjac, M. muntjak
 * Genus: Rusa
 * Rusa deer, R. timorensis
 * Sambar deer, R. unicolor

Locally extinct
The following taxa are locally extinct in the country:
 * Wild water buffalo, Bubalus arnee
 * Bali tiger and Javan tiger, both Panthera tigris sondaica populations