This article contains the list of Indonesian endemic freshwater fishes. Indonesia is a country with vast amount of freshwater fish species; it is the country with the third-largest number of freshwater fish species in the world, with a total of 1155 species. And about 440 species are endemic to Indonesia. This makes Indonesia as the 4th country with the largest endemic freshwater fish species, with Brazil (1716 species) in the 1st place, China (888) in the 2nd place and USA (593 species) in the 3rd place. (Dody94 2011)
Below is the list of Indonesian endemic freshwater fishes:
| Species name | Family | Vernacular name | Other name | Year found | |
|---|---|---|---|---|---|
| Acrochordonichthys chamaeleon | Akysidae | N/A | N/A | N/A | |
| Acrochordonichthys guttatus | Akysidae | N/A | N/A | N/A | |
| Acrochordonichthys mahakamensis | Akysidae | N/A | N/A | N/A | |
| Acrochordonichthys pleurostigma | Akysidae | N/A | N/A | N/A | |
| Acrochordonichthys strigosus | Akysidae | N/A | N/A | N/A | |
| Adrianichthys kruyti | Adrianichthyidae | Duckbilled Buntingi | N/A | N/A | |
| Adrianichthys roseni | Adrianichthyidae | Rosen's Butingi | N/A | 2004 | |
| Akysis fuscus | Akysidae | N/A | N/A | N/A | |
| Akysis galeatus | Akysidae | N/A | N/A | 2007 | |
| Akysis heterurus | Akysidae | N/A | N/A | N/A | |
| Akysis macronemus | Akysidae | N/A | N/A | N/A | |
| Akysis pseudobagarius | Akysidae | N/A | N/A | N/A | |
| Akysis scorteus | Akysidae | N/A | N/A | 2007 | |
| Allomogurnda sampricei | Eleotridae | N/A | N/A | 2003 | |
| Arius goniaspis OC | Ariidae | Blacktip Sea Catfish | N/A | N/A | |
| Arius macronotacanthus OC | Ariidae | N/A | N/A | N/A | |
| Arius nudidens | Ariidae | N/A | N/A | N/A | |
| Auriglobus amabilis | Tetraodontidae | N/A | N/A | N/A | |
| Awaous personatus OC | Gobiidae | N/A | N/A | N/A | |
| Bagrichthys micranodus | Bagridae | N/A | N/A | N/A | |
| Bagrichthys vaillantii | Bagridae | N/A | N/A | N/A | |
| Barbodes mahakkamensis | Cyprinidae | N/A | N/A | N/A | |
| Barbodes platysoma | Cyprinidae | N/A | N/A | N/A | |
| Barilius borneensis | Cyprinidae | N/A | N/A | N/A | |
| Betta albimarginata | Osphronemidae | White-edged Betta | N/A | N/A | |
| Betta antoni | Osphronemidae | N/A | N/A | 2006 | |
| Betta aurigans | Osphronemidae | N/A | N/A | 2004 | |
| Betta breviobesus | Osphronemidae | N/A | N/A | N/A | |
| Betta burdigala | Osphronemidae | Red Brown Dwarf Fighter | N/A | N/A | |
| Betta channoides | Osphronemidae | Snakehead Betta | N/A | N/A | |
| Betta chloropharynx | Osphronemidae | Greenthroat Mouthbrooder | N/A | N/A | |
| Betta coccina | Osphronemidae | Wine Red Betta | N/A | N/A | |
| Betta compuncta | Osphronemidae | N/A | N/A | 2006 | |
| Betta cracens | Osphronemidae | Clownface Betta | N/A | 2005 | |
| Betta dimidiata | Osphronemidae | Dwarf Mouthbrooder | N/A | N/A | |
| Betta edithae | Osphronemidae | Edith's Mouthbrooder | N/A | N/A | |
| Betta enisae | Osphronemidae | Longfin Betta | N/A | N/A | |
| Betta falx | Osphronemidae | Sumatra Betta | N/A | N/A | |
| Betta foerschi | Osphronemidae | Foersch's Mouthbrooder | N/A | N/A | |
| Betta ideii | Osphronemidae | Sakura Betta | N/A | 2006 | |
| Betta krataios | Osphronemidae | Kapuas Betta | N/A | 2006 | |
| Betta mandor | Osphronemidae | N/A | N/A | 2006 | |
| Betta miniopinna | Osphronemidae | Smallfin Fighter | N/A | N/A | |
| Betta obscura | Osphronemidae | N/A | N/A | 2005 | |
| Betta pallifina | Osphronemidae | Barito Betta | N/A | 2005 | |
| Betta patoti | Osphronemidae | Black Betta | N/A | N/A | |
| Betta picta OC | Osphronemidae | Spotted Betta | N/A | N/A | |
| Betta pinguis | Osphronemidae | N/A | N/A | N/A | |
| Betta raja | Osphronemidae | Raja Betta | N/A | 2005 | |
| Betta renata | Osphronemidae | N/A | N/A | N/A | |
| Betta rubra | Osphronemidae | Toba Betta | N/A | N/A | |
| Betta rutilans | Osphronemidae | Reddish Dwarf Fighter | N/A | N/A | |
| Betta schalleri | Osphronemidae | Schaller's Mouthbrooder | N/A | N/A | |
| Betta simorum | Osphronemidae | Simor Fighter | N/A | N/A | |
| Betta spilotogena | Osphronemidae | Double Lipspot Mouthbrooder | N/A | N/A | |
| Betta strohi | Osphronemidae | Father Stroh's Mouthbrooder | N/A | N/A | |
| Betta uberis | Osphronemidae | N/A | N/A | 2006 | |
| Boraras brigittae | Cyprinidae | Redfin Dwarf Rasbora | N/A | N/A | |
| Boraras merah | Cyprinidae | N/A | N/A | N/A | |
| Bostrichthys aruensis | Eleotridae | Island Gudgeon | N/A | N/A | |
| Bostrychus microphthalmus | Eleotridae | N/A | N/A | 2005 | |
| Botia macracanthus OC | Cobitidae | Clown Loach | N/A | N/A | |
| Brachygobius xanthozona | Gobiidae | Bumblebee Goby | N/A | N/A | |
| Breitensteinia cessator | Akysidae | N/A | N/A | N/A | |
| Breitensteinia hypselurus | Akysidae | N/A | N/A | N/A | |
| Breitensteinia insignis | Akysidae | N/A | N/A | N/A | |
| Callogobius stellatus | Gobiidae | N/A | N/A | N/A | |
| Carinotetraodon irrubesco | Tetraodontidae | Redtailed Redeye Puffer | |||
| Channa cyanospilos | Channidae | Bluespotted Snakehead | |||
| Channa melanoptera OC | Channidae | Blackfinned Snakehead | |||
| Channa pleurophthalmus | Channidae | Ocellated Snakehead | |||
| Chendol lubricus | Chaudhuriidae | N/A | |||
| Chilatherina alleni | Melanotaeniidae | Allen's Rainbowfish | |||
| Chilatherina bleheri | Melanotaeniidae | Bleher's Rainbowfish | |||
| Chilatherina pricei | Melanotaeniidae | Price's Rainbowfish | |||
| Chilatherina sentaniensis | Melanotaeniidae | Sentani Rainbowfish | |||
| Chitala hypselonotus | Notopteridae | N/A | |||
| Clarias insolitus | Clariidae | N/A | N/A | 2003 | |
| Clarias intermedius | Clariidae | N/A | |||
| Clarias kapuasensis | Clariidae | N/A | |||
| Clarias leiacanthus OC | Clariidae | N/A | |||
| Clarias microstomus | Clariidae | N/A | |||
| Clarias nigricans | Clariidae | N/A | N/A | 2003 | |
| Clarias olivaceus | Clariidae | N/A | |||
| Clarias pseudoleiacanthus | Clariidae | N/A | |||
| Clarias pseudonieuhofii | Clariidae | N/A | N/A | 2004 | |
| Clupeichthys bleekeri | Clupeidae | Kapuas River Sprat | |||
| Clupeoides hypselosoma | Clupeidae | Kalimantan River Sprat | |||
| Craterocephalus fistularis | Atherinidae | Lake Triton Hardyhead | |||
| Crossocheilus gnathopogon | Cyprinidae | N/A | |||
| Cyclocheilichthys janthochir | Cyprinidae | Redfin River Barb | |||
| Dermogenys ontana | Hemiramphidae | Mountain Halfbeak | |||
| Dermogenys orientalis | Hemiramphidae | N/A | |||
| Dermogenys sumatrana OC | Hemiramphidae | Sumatra Halfbeak | |||
| Dermogenys vogti | Hemiramphidae | N/A | |||
| Diplocheilichthys jentinkii | Cyprinidae | N/A | |||
| Doryichthys heterosoma | Syngnathidae | N/A | |||
| Eirmotus furvus | Cyprinidae | N/A | N/A | 2008 | |
| Eirmotus insignis | Cyprinidae | N/A | N/A | 2008 | |
| Eirmotus isthmus | Cyprinidae | N/A | N/A | 2008 | |
| Eleotris brachyurus | Eleotridae | N/A | |||
| Eleotris melanura | Eleotridae | N/A | |||
| Eleotris pseudacanthopomus | Eleotridae | N/A | |||
| Encheloclarias baculum | Clariidae | N/A | |||
| Encheloclarias tapeinopterus | Clariidae | N/A | |||
| Encheloclarias velatus | Clariidae | N/A | |||
| Gastromyzon contractus | Balitoridae | N/A | |||
| Gastromyzon embalohensis | Balitoridae | N/A | |||
| Gastromyzon praestans | Balitoridae | N/A | N/A | 2006 | |
| Gastromyzon psiloetron | Balitoridae | N/A | N/A | 2006 | |
| Gastromyzon russulus | Balitoridae | N/A | N/A | 2006 | |
| Gastromyzon zebrinus | Balitoridae | N/A | N/A | 2006 | |
| Glossamia beauforti OC | Apogonidae | Beaufort's Mouth Almighty | |||
| Glossamia heurni | Apogonidae | N/A | |||
| Glossogobius flavipinnis | Gobiidae | N/A | |||
| Glossogobius hoesei | Gobiidae | Hoese's Goby | N/A | N/A | |
| Glossogobius intermedius | Gobiidae | N/A | |||
| Glossogobius matanensis | Gobiidae | N/A | |||
| Glossolepis dorityi | Melanotaeniidae | Grime Rainbowfish | |||
| Glossolepis incisus OC | Melanotaeniidae | Salmon-red Rainbowfish | |||
| Glossolepis leggetti | Melanotaeniidae | Leggett's Rainbowfish | |||
| Glossolepis pseudoincisus | Melanotaeniidae | Tami River Rainbowfish | |||
| Glyptothorax exodon | Sisoridae | N/A | N/A | 2005 | |
| Glyptothorax nieuwenhuisi | Sisoridae | N/A | |||
| Glyptothorax platypogon OC | Sisoridae | Brown Hillstream Catfish | N/A | N/A | |
| Glyptothorax plectilis | Sisoridae | N/A | N/A | 2008 | |
| Glyptothorax schmidti | Sisoridae | N/A | |||
| Glyptothorax tiong | Sisoridae | N/A | |||
| Gobius tigrellus | Gobiidae | Tiger Goby | |||
| Gymnochanda flamea | Ambassidae | N/A | |||
| Gymnochanda limi | Ambassidae | N/A | |||
| Gyrinocheilus pustulosus | Gyrinocheilidae | N/A | |||
| Helicophagus typus | Pangasiidae | N/A | |||
| Hemibagrus bongan OC | Bagridae | N/A | |||
| Hemibagrus caveatus | Bagridae | N/A | |||
| Hemibagrus olyroides | Bagridae | N/A | |||
| Hemibagrus velox | Bagridae | N/A | |||
| Hemileiocassis panjang | Bagridae | N/A | |||
| Hemirhamphodon chrysopunctatus | Hemiramphidae | Gold-spot Halfbeak | |||
| Hemirhamphodon kapuasensis | Hemiramphidae | Red-striped Halfbeak | |||
| Hemirhamphodon phaiosoma | Hemiramphidae | Long-finned Halfbeak | |||
| Hemirhamphodon tengah | Hemiramphidae | Oviparous Halfbeak | |||
| Hemisilurus moolenburghi | Siluridae | N/A | |||
| Hephaestus lineatus | Terapontidae | Lined Grunter | |||
| Homaloptera gymnogaster | Balitoridae | N/A | |||
| Homaloptera heterolepis | Balitoridae | N/A | |||
| Homaloptera ocellata | Balitoridae | N/A | |||
| Homaloptera ripleyi | Balitoridae | N/A | |||
| Homaloptera vanderbilti | Balitoridae | N/A | |||
| Homaloptera yuwonoi | Balitoridae | N/A | |||
| Hyalobagrus flavus | Bagridae | Shadow Catfish | |||
| Hyalobagrus leiacanthus | Bagridae | N/A | |||
| Hypergastromyzon humilis | Balitoridae | N/A | |||
| Ilisha pristigastroides OC | Pristigasteridae | N/A | |||
| Kalimantania lawak | Cyprinidae | N/A | |||
| Kalyptatherina helodes | Telmatherinidae | Marine Sailfin Silverside | |||
| Kottelatlimia hipporhynchos | Cobitidae | N/A | N/A | 2008 | |
| Kryptopterus lumholtzi | Siluridae | N/A | |||
| Kryptopterus minor | Siluridae | Ghost Catfish | |||
| Kryptopterus mononema | Siluridae | N/A | |||
| Kryptopterus piperatus | Siluridae | N/A | N/A | 2004 | |
| Labeo moszkowskii | Cyprinidae | N/A | |||
| Labeo pietschmanni | Cyprinidae | N/A | |||
| Labiobarbus lamellifer | Cyprinidae | N/A | |||
| Lagusia micracanthus | Terapontidae | N/A | |||
| Leiocassis aculeatus | Bagridae | N/A | N/A | 2005 | |
| Leiocassis macropterus | Bagridae | N/A | |||
| Leiocassis tenebricus | Bagridae | N/A | N/A | 2006 | |
| Lentipes adelphizonus | Gobiidae | N/A | N/A | 2006 | |
| Lentipes crittersius | Gobiidae | N/A | |||
| Lentipes dimetrodon | Gobiidae | N/A | |||
| Lentipes multiradiatus | Gobiidae | N/A | |||
| Lentipes whittenorum | Gobiidae | N/A | |||
| Lepidocephalichthys lorentzi | Cobitidae | N/A | |||
| Lepidocephalus spectrum | Cobitidae | N/A | |||
| Leptachirus lorentz | Soleidae | N/A | N/A | 2007 | |
| Leptobarbus hoevenii | Cyprinidae | N/A | |||
| Leptobarbus melanopterus | Cyprinidae | N/A | |||
| Lobocheilos ixocheilos | Cyprinidae | N/A | N/A | 2008 | |
| Lobocheilos lehat | Cyprinidae | N/A | |||
| Lobocheilos schwanenfeldii OC | Cyprinidae | N/A | |||
| Lobocheilos tenura | Cyprinidae | N/A | N/A | 2008 | |
| Luciocephalus aura | Osphronemidae | N/A | N/A | 2005 | |
| Marosatherina ladigesi OC | Telmatherinidae | Celebes Rainbowfish | |||
| Melanotaenia ajamaruensis | Melanotaeniidae | Ajamaru Lakes Rainbowfish | |||
| Melanotaenia ammeri | Melanotaeniidae | N/A | N/A | 2008 | |
| Melanotaenia angfa | Melanotaeniidae | Yakati Rainbowfish | Angfa Rainbowfish | ||
| Melanotaenia arfakensis | Melanotaeniidae | Arfak Rainbowfish | |||
| Melanotaenia batanta | Melanotaeniidae | Batanta Rainbowfish | |||
| Melanotaenia boesemani | Melanotaeniidae | Boeseman's Rainbowfish | |||
| Melanotaenia catherinae | Melanotaeniidae | Waigeo Rainbowfish | |||
| Melanotaenia corona | Melanotaeniidae | Corona Rainbowfish | |||
| Melanotaenia fredericki | Melanotaeniidae | Sorong Rainbowfish | |||
| Melanotaenia irianjaya | Melanotaeniidae | Irian Jaya Rainbowfish | |||
| Melanotaenia japenensis | Melanotaeniidae | Japen Rainbowfish | |||
| Melanotaenia kamaka | Melanotaeniidae | Kamaka Rainbowfish | |||
| Melanotaenia kokasensis | Melanotaeniidae | N/A | N/A | 2008 | |
| Melanotaenia lakamora | Melanotaeniidae | Lakamora Rainbowfish | |||
| Melanotaenia maylandi | Melanotaeniidae | Mayland's Rainbowfish | |||
| Melanotaenia misoolensis | Melanotaeniidae | Misool Rainbowfish | |||
| Melanotaenia ogilbyi OC | Melanotaeniidae | Ogilby's Rainbowfish | |||
| Melanotaenia parva | Melanotaeniidae | Lake Kurumoi Rainbowfish | |||
| Melanotaenia pierucciae | Melanotaeniidae | Pierucci's Rainbowfish | |||
| Melanotaenia praecox OC | Melanotaeniidae | Neon Rainbowfish | |||
| Melanotaenia rubripinnis | Melanotaeniidae | Red-finned Rainbowfish | |||
| Melanotaenia synergos | Melanotaeniidae | N/A | N/A | 2008 | |
| Melanotaenia vanheurni | Melanotaeniidae | Van Heurn's Rainbowfish | N/A | N/A | |
| Microphis caudocarinatus | Syngnathidae | Slender Pipefish | N/A | N/A | |
| Mogurnda aiwasoensis | Eleotridae | N/A | N/A | N/A | |
| Mogurnda kaifayama | Eleotridae | N/A | N/A | N/A | |
| Mogurnda magna | Eleotridae | N/A | N/A | N/A | |
| Mogurnda mbuta | Eleotridae | N/A | N/A | N/A | |
| Mogurnda pardalis | Eleotridae | N/A | N/A | N/A | |
| Mogurnda wapoga | Eleotridae | N/A | N/A | N/A | |
| Mugilogobius adeia | Gobiidae | N/A | N/A | N/A | |
| Mugilogobius amadi | Gobiidae | N/A | N/A | N/A | |
| Mugilogobius karatunensis | Gobiidae | N/A | N/A | N/A | |
| Mugilogobius latifrons | Gobiidae | N/A | N/A | N/A | |
| Mugilogobius lepidotus | Gobiidae | N/A | N/A | N/A | |
| Mugilogobius rexi | Gobiidae | N/A | N/A | N/A | |
| Mugilogobius sarasinorum | Gobiidae | Sarasin's Goby | N/A | N/A | |
| Mugilogobius zebra OC | Gobiidae | N/A | N/A | N/A | |
| Mystacoleucus padangensis | Cyprinidae | N/A | N/A | N/A | |
| Mystus abbreviatus | Bagridae | N/A | N/A | N/A | |
| Mystus alasensis | Bagridae | N/A | N/A | 2005 | |
| Mystus bimaculatus OC | Bagridae | N/A | N/A | ||
| Mystus impluviatus | Bagridae | N/A | N/A | 2003 | |
| Mystus punctifer | Bagridae | N/A | N/A | N/A | |
| Nandus mercatus | Nandidae | N/A | N/A | 2008 | |
| Nanobagrus armatus | Bagridae | N/A | N/A | N/A | |
| Nanobagrus immaculatus | Bagridae | N/A | N/A | 2008 | |
| Nanobagrus stellatus | Bagridae | N/A | N/A | N/A | |
| Nanobagrus torquatus | Bagridae | N/A | N/A | 2008 | |
| Nemacheilus chrysolaimos | Balitoridae | N/A | N/A | N/A | |
| Nemacheilus lactogeneus | Balitoridae | N/A | N/A | N/A | |
| Nemacheilus longipinnis | Balitoridae | N/A | N/A | N/A | |
| Nemacheilus pfeifferae | Balitoridae | N/A | N/A | N/A | |
| Nemacheilus tuberigum | Balitoridae | N/A | N/A | N/A | |
| Neogastromyzon kottelati | Balitoridae | N/A | N/A | 2006 | |
| Neolissochilus longipinnis | Cyprinidae | N/A | N/A | N/A | |
| Neolissochilus sumatranus OC | Cyprinidae | Large-scaled Barb | N/A | N/A | |
| Neolissochilus thienemanni | Cyprinidae | N/A | N/A | N/A | |
| Neostethus djajaorum | Phallostethidae | N/A | N/A | N/A | |
| Nomorhamphus australis | Hemiramphidae | Hooked Halfbeak | N/A | N/A | |
| Nomorhamphus brembachi | Hemiramphidae | N/A | N/A | N/A | |
| Nomorhamphus celebensis | Hemiramphidae | Northern Harlequin Halfbeak | N/A | N/A | |
| Nomorhamphus ebrardtii | Hemiramphidae | Orange Finned Halfbeak | N/A | N/A | |
| Nomorhamphus hageni | Hemiramphidae | N/A | N/A | N/A | |
| Nomorhamphus kolonodalensis | Hemiramphidae | N/A | N/A | N/A | |
| Nomorhamphus liemi | Hemiramphidae | Southern Harlequin Halfbeak | N/A | N/A | |
| Nomorhamphus megarrhamphus | Hemiramphidae | N/A | N/A | N/A | |
| Nomorhamphus ravnaki | Hemiramphidae | Turquoise Halfbeak | N/A | N/A | |
| Nomorhamphus sanussii | Hemiramphidae | N/A | N/A | N/A | |
| Nomorhamphus towoetii | Hemiramphidae | Towoeti Halfbeak | N/A | N/A | |
| Nomorhamphus weberi | Hemiramphidae | N/A | N/A | N/A | |
| Ompok binotatus | Siluridae | N/A | N/A | N/A | |
| Ompok javanensis | Siluridae | N/A | N/A | N/A | |
| Ompok miostoma | Siluridae | N/A | N/A | N/A | |
| Ompok pluriradiatus | Siluridae | N/A | N/A | N/A | |
| Ompok supernus | Siluridae | N/A | N/A | 2008 | |
| Ompok weberi | Siluridae | N/A | N/A | N/A | |
| Oryzias bonneorum | Adrianichthyidae | Bonnes’ Butingi | N/A | 2008 | |
| Oryzias celebensis | Adrianichthyidae | Celebes Medaka | N/A | N/A | |
| Oryzias hubbsi | Adrianichthyidae | Hubbs's Medaka | N/A | N/A | |
| Oryzias marmoratus | Adrianichthyidae | Javanese Ricefish | N/A | N/A | |
| Oryzias matanensis | Adrianichthyidae | Matano Medaka | N/A | N/A | |
| Oryzias nebulosus | Adrianichthyidae | Nebulous Ricefish | N/A | 2004 | |
| Oryzias nigrimas | Adrianichthyidae | Black Buntingi | N/A | N/A | |
| Oryzias orthognathus | Adrianichthyidae | Sharpjawed Buntingi | N/A | N/A | |
| Oryzias profundicola | Adrianichthyidae | Yellow-finned Medaka | N/A | N/A | |
| Osteochilus bellus | Cyprinidae | N/A | N/A | N/A | |
| Osteochilus bleekeri | Cyprinidae | N/A | N/A | 2008 | |
| Osteochilus borneensis | Cyprinidae | N/A | N/A | N/A | |
| Osteochilus intermedius | Cyprinidae | N/A | N/A | N/A | |
| Osteochilus jeruk | Cyprinidae | N/A | N/A | N/A | |
| Osteochilus kappenii | Cyprinidae | N/A | N/A | N/A | |
| Osteochilus kelabau | Cyprinidae | N/A | N/A | N/A | |
| Osteochilus kuekenthali | Cyprinidae | N/A | N/A | N/A | |
| Osteochilus partilineatus | Cyprinidae | N/A | N/A | N/A | |
| Osteochilus pentalineatus | Cyprinidae | N/A | N/A | N/A | |
| Osteochilus pleurotaenia OC | Cyprinidae | N/A | N/A | N/A | |
| Osteochilus repang | Cyprinidae | N/A | N/A | N/A | |
| Osteochilus serokan | Cyprinidae | N/A | N/A | N/A | |
| Oxyeleotris altipinna | Eleotridae | N/A | N/A | N/A | |
| Oxyeleotris urophthalmoides OC | Eleotridae | N/A | N/A | N/A | |
| Oxyeleotris wisselensis | Eleotridae | Paniai Gudgeon | N/A | N/A | |
| Paedocypris carbunculus | Cyprinidae | N/A | N/A | 2008 | |
| Paedocypris progenetica | Cyprinidae | N/A | N/A | 2006 | |
| Pandaka rouxi | Gobiidae | N/A | N/A | N/A | |
| Pangasius bedado | Pangasiidae | N/A | N/A | N/A | |
| Pangasius humeralis | Pangasiidae | N/A | N/A | N/A | |
| Pangasius lithostoma | Pangasiidae | N/A | N/A | N/A | |
| Pangasius mahakamensis | Pangasiidae | N/A | N/A | N/A | |
| Pangasius nieuwenhuisii | Pangasiidae | N/A | N/A | N/A | |
| Pangasius rheophilus | Pangasiidae | N/A | N/A | N/A | |
| Pangio alternans | Cobitidae | Borneo Kuhli Loach | N/A | N/A | |
| Pangio pulla | Cobitidae | Red Giant Kuhli Loach | N/A | N/A | |
| Pangio robiginosa | Cobitidae | N/A | N/A | N/A | |
| Pangio superba | Cobitidae | N/A | N/A | N/A | |
| Parachela cyanea | Cyprinidae | N/A | N/A | N/A | |
| Parachela ingerkongi | Cyprinidae | N/A | N/A | N/A | |
| Paradoxodacna piratica | Ambassidae | N/A | N/A | N/A | |
| Parakysis anomalopteryx | Parakysidae | N/A | N/A | N/A | |
| Parakysis notialis | Parakysidae | N/A | N/A | N/A | |
| Parambassis altipinnis | Ambassidae | High-finned Glass Perchlet | N/A | N/A | |
| Parambassis macrolepis | Ambassidae | N/A | N/A | N/A | |
| Paratherina cyanea | Telmatherinidae | N/A | N/A | N/A | |
| Paratherina labiosa | Telmatherinidae | N/A | N/A | N/A | |
| Paratherina striata | Telmatherinidae | N/A | N/A | N/A | |
| Paratherina wolterecki | Telmatherinidae | N/A | N/A | N/A | |
| Parosphromenus anjunganensis | Osphronemidae | Anjungan Licorice Gourami | N/A | N/A | |
| Parosphromenus bintan | Osphronemidae | Bintan Licorice Gourami | N/A | N/A | |
| Parosphromenus deissneri OC | Osphronemidae | Licorice Gourami | N/A | N/A | |
| Parosphromenus filamentosus | Osphronemidae | Spiketail Licorice Gourami | N/A | N/A | |
| Parosphromenus linkei | Osphronemidae | Linke's Licorice Gourami | N/A | N/A | |
| Parosphromenus opallios | Osphronemidae | N/A | N/A | 2005 | |
| Parosphromenus ornaticauda | Osphronemidae | Redtail Licorice Gourami | N/A | N/A | |
| Parosphromenus pahuensis | Osphronemidae | N/A | N/A | 2005 | |
| Parosphromenus parvulus | Osphronemidae | Small Licorice Gourami | N/A | N/A | |
| Parosphromenus quindecim | Osphronemidae | N/A | N/A | 2005 | |
| Parosphromenus sumatranus | Osphronemidae | Fire Red Licorice Gourami | N/A | N/A | |
| Pectenocypris balaena | Cyprinidae | N/A | N/A | N/A | |
| Pectenocypris korthausae | Cyprinidae | Orange Doublespotted Rasbora | N/A | N/A | |
| Pelangia mbutaensis | Melanotaeniidae | Lake Mbuta Rainbowfish | N/A | N/A | |
| Pisodonophis hypselopterus | Ophichthidae | N/A | N/A | N/A | |
| Polydactylus macrophthalmus | Polynemidae | River Threadfin | N/A | N/A | |
| Polynemus kapuasensis | Polynemidae | N/A | N/A | 2003 | |
| Poropuntius tawarensis | Cyprinidae | N/A | N/A | N/A | |
| Pristolepis grootii OC | Nandidae | Indonesian Leaffish | N/A | N/A | |
| Pseudeutropius brachypopterus | Schilbeidae | N/A | N/A | N/A | |
| Pseudeutropius moolenburghae | Schilbeidae | N/A | N/A | N/A | |
| Pseudobagarius meridionalis | Akysidae | N/A | N/A | 2004 | |
| Pseudogobiopsis penango | Gobiidae | N/A | N/A | N/A | |
| Pseudomugil ivantsoffi | Pseudomugilidae | N/A | N/A | N/A | |
| Pseudomugil pellucidus | Pseudomugilidae | Transparent Blue-eye | N/A | N/A | |
| Pseudomugil reticulatus | Pseudomugilidae | Vogelkop Blue-eye | N/A | N/A | |
| Pseudomystus breviceps | Bagridae | N/A | N/A | N/A | |
| Pseudomystus carnosus | Bagridae | N/A | N/A | 2005 | |
| Pseudomystus flavipinnis | Bagridae | N/A | N/A | N/A | |
| Pseudomystus heokhuii | Bagridae | N/A | N/A | 2008 | |
| Pseudomystus mahakamensis | Bagridae | N/A | N/A | N/A | |
| Pseudomystus moeschii | Bagridae | N/A | N/A | N/A | |
| Pseudomystus myersi | Bagridae | N/A | N/A | N/A | |
| Pseudomystus rugosus OC | Bagridae | N/A | N/A | N/A | |
| Pseudomystus stenogrammus | Bagridae | N/A | N/A | 2005 | |
| Pseudomystus vaillanti | Bagridae | N/A | N/A | N/A | |
| Puntius anchisporus | Cyprinidae | N/A | N/A | N/A | |
| Puntius aphya | Cyprinidae | N/A | N/A | N/A | |
| Puntius bunau | Cyprinidae | N/A | N/A | 2005 | |
| Puntius dorsimaculatus | Cyprinidae | Blackline Barb | N/A | N/A | |
| Puntius endecanalis | Cyprinidae | N/A | N/A | N/A | |
| Puntius foerschi | Cyprinidae | N/A | N/A | N/A | |
| Puntius gemellus | Cyprinidae | N/A | N/A | N/A | |
| Puntius microps | Cyprinidae | N/A | N/A | N/A | |
| Puntius oligolepis IN | Cyprinidae | Checkered Barb | N/A | N/A | |
| Puntius rhomboocellatus OC | Cyprinidae | Round-banded Barb | N/A | N/A | |
| Puntius trifasciatus | Cyprinidae | N/A | N/A | N/A | |
| Rasbora aprotaenia | Cyprinidae | N/A | N/A | N/A | |
| Rasbora baliensis | Cyprinidae | N/A | N/A | N/A | |
| Rasbora beauforti | Cyprinidae | Spotlight Rasbora | N/A | N/A | |
| Rasbora borneensis | Cyprinidae | N/A | N/A | N/A | |
| Rasbora bunguranensis OC | Cyprinidae | N/A | N/A | N/A | |
| Rasbora dies | Cyprinidae | N/A | N/A | 2008 | |
| Rasbora ennealepis | Cyprinidae | N/A | N/A | N/A | |
| Rasbora jacobsoni | Cyprinidae | N/A | N/A | N/A | |
| Rasbora johannae | Cyprinidae | N/A | N/A | N/A | |
| Rasbora kalbarensis | Cyprinidae | Kalbar Rasbora | N/A | N/A | |
| Rasbora laticlavia | Cyprinidae | N/A | N/A | N/A | |
| Rasbora leptosoma | Cyprinidae | Copperstripe Rasbora | N/A | N/A | |
| Rasbora reticulata | Cyprinidae | Reticulate Rasbora | N/A | N/A | |
| Rasbora spilotaenia | Cyprinidae | N/A | N/A | N/A | |
| Rasbora subtilis | Cyprinidae | N/A | N/A | N/A | |
| Rasbora tawarensis | Cyprinidae | N/A | N/A | N/A | |
| Rasbora tobana | Cyprinidae | N/A | N/A | N/A | |
| Rasbora vulcanus | Cyprinidae | N/A | N/A | N/A | |
| Redigobius amblyrhynchus | Gobiidae | N/A | N/A | N/A | |
| Redigobius leptochilus | Gobiidae | N/A | N/A | N/A | |
| Schismatorhynchos endecarhapis | Cyprinidae | N/A | N/A | N/A | |
| Schismatorhynchos heterorhynchos OC | Cyprinidae | Dolphin Barb | N/A | N/A | |
| Schistura maculiceps | Balitoridae | N/A | N/A | N/A | |
| Scleropages aureus | Osteoglossidae | Gold Arowana | N/A | 2003 | |
| Scleropages legendrei | Osteoglossidae | Red Arowana | N/A | 2003 | |
| Scleropages macrocephalus | Osteoglossidae | Silver Asian Arowana | N/A | 2003 | |
| Sicyopterus hageni | Gobiidae | Hagen's Goby | N/A | N/A | |
| Sicyopterus parvei | Gobiidae | N/A | N/A | N/A | |
| Sicyopus exallisquamulus | Gobiidae | N/A | N/A | 2006 | |
| Sicyopus multisquamatus | Gobiidae | N/A | N/A | N/A | |
| Sicyopus mystax | Gobiidae | N/A | N/A | N/A | |
| Silurichthys citatus | Siluridae | N/A | N/A | N/A | |
| Silurichthys gibbiceps | Siluridae | N/A | N/A | N/A | |
| Silurichthys sanguineus | Siluridae | N/A | N/A | N/A | |
| Sphaerichthys acrostoma | Osphronemidae | Large Chocolate Gourami | N/A | N/A | |
| Sphaerichthys selatanensis | Osphronemidae | Selatan Chocolate Gourami | N/A | N/A | |
| Sphaerichthys vaillanti | Osphronemidae | Vaillant's Chocolate Gourami | N/A | N/A | |
| Stenogobius blokzeyli OC | Gobiidae | N/A | N/A | N/A | |
| Stenogobius lachneri | Gobiidae | Bintuni Goby | N/A | N/A | |
| Stenogobius zurstrassenii | Gobiidae | N/A | N/A | N/A | |
| Stigmatogobius signifer | Gobiidae | N/A | N/A | 2005 | |
| Stiphodon carisa | Gobiidae | N/A | N/A | 2008 | |
| Stiphodon ornatus | Gobiidae | N/A | N/A | N/A | |
| Stiphodon weberi | Gobiidae | N/A | N/A | N/A | |
| Stiphodon zebrinus | Gobiidae | N/A | N/A | N/A | |
| Sundadanio axelrodi | Cyprinidae | Axelrod's Fire Rasbora | N/A | N/A | |
| Sundagagata robusta | Sisoridae | N/A | N/A | N/A | |
| Sundasalanx malleti | Sundasalangidae | N/A | N/A | N/A | |
| Sundasalanx megalops | Sundasalangidae | N/A | N/A | N/A | |
| Sundasalanx mesops | Sundasalangidae | N/A | N/A | N/A | |
| Sundasalanx microps OC | Sundasalangidae | N/A | N/A | N/A | |
| Sundasalanx platyrhynchus | Sundasalangidae | N/A | N/A | N/A | |
| Sundoreonectes obesus | Balitoridae | N/A | N/A | N/A | |
| Telmatherina abendanoni | Telmatherinidae | Matano Celebes Rainbowfish | N/A | N/A | |
| Telmatherina antoniae | Telmatherinidae | N/A | N/A | N/A | |
| Telmatherina bonti | Telmatherinidae | Lake Towuti Rainbowfish | N/A | N/A | |
| Telmatherina celebensis | Telmatherinidae | N/A | N/A | N/A | |
| Telmatherina obscura | Telmatherinidae | N/A | N/A | N/A | |
| Telmatherina opudi | Telmatherinidae | N/A | N/A | N/A | |
| Telmatherina prognatha | Telmatherinidae | N/A | N/A | N/A | |
| Telmatherina sarasinorum | Telmatherinidae | N/A | N/A | N/A | |
| Telmatherina wahjui | Telmatherinidae | N/A | N/A | N/A | |
| Tetranesodon conorhynchus | Ariidae | Lorentz Catfish | N/A | N/A | |
| Tetraodon waandersii | Tetraodontidae | N/A | N/A | N/A | |
| Thryssocypris ornithostoma | Cyprinidae | N/A | N/A | N/A | |
| Thryssocypris smaragdinus | Cyprinidae | N/A | N/A | N/A | |
| Thynnichthys polylepis | Cyprinidae | N/A | N/A | N/A | |
| Thynnichthys vaillanti | Cyprinidae | N/A | N/A | N/A | |
| Tominanga aurea | Telmatherinidae | N/A | N/A | N/A | |
| Tominanga sanguicauda | Telmatherinidae | Blood-tail Rainbowfish | N/A | N/A | |
| Tondanichthys kottelati | Hemiramphidae | Kottelat's Halfbeak | N/A | N/A | |
| Trigonostigma hengeli OC | Cyprinidae | Glowlight Rasbora | N/A | N/A | |
| Tryphauchenopsis intermedius | Gobiidae | N/A | N/A | N/A | |
| Vaillantella cinnamomea | Balitoridae | Brown Forktail Loach | N/A | N/A | |
| Variichthys jamoerensis | Terapontidae | Jamur Lake Grunter | Yamur Lake Grunter | N/A | |
| Xenopoecilus oophorus | Adrianichthyidae | Eggcarrying Butingi | N/A | N/A | |
| Xenopoecilus poptae | Adrianichthyidae | Popta's Butingi | N/A | N/A | |
| Xenopoecilus sarasinorum | Adrianichthyidae | Sarasin's Minnow | N/A | N/A | |
| Yirrkala gjellerupi | Ophichthidae | N/A | N/A | N/A | |
| Zenarchopterus alleni | Hemiramphidae | Allen's River Garfish | N/A | N/A | |
| Zenarchopterus ornithocephala | Hemiramphidae | Vogelkop River Garfish | N/A | N/A | |
| Zenarchopterus xiphophorus | Hemiramphidae | N/A | N/A | N/A | |
| Species name | Family | Vernacular name | Other name | Year found |