| Species name | Family | Vernacular name | Other name | Year found |
| Acrochordonichthys chamaeleon | Akysidae | Baung-kali kapuas | N/A | N/A |
| Acrochordonichthys guttatus | Akysidae | Baung-kali barito | N/A | N/A |
| Acrochordonichthys mahakamensis | Akysidae | Baung-kali mahakam | N/A | N/A |
| Acrochordonichthys rugosus | Akysidae | Baung-kali banjo | N/A | N/A |
| Acrochordonichthys strigosus | Akysidae | Baung-kali kasar | N/A | N/A |
| Adrianichthys kruyti | Adrianichthyidae | Buntingi paruh-itik | N/A | N/A |
| Adrianichthys roseni | Adrianichthyidae | Buntingi rosen | N/A | 2004 |
| Akysis fuscus | Akysidae | Jakaripuh merah | N/A | N/A |
| Akysis galeatus | Akysidae | Jakaripuh besar | N/A | 2007 |
| Akysis heterurus | Akysidae | Jakaripuh batang-hari | N/A | N/A |
| Akysis macronemus | Akysidae | Jakaripuh kumis-panjang | N/A | N/A |
| Akysis pseudobagarius | Akysidae | Jakaripuh kelaling | N/A | N/A |
| Akysis scorteus | Akysidae | Jakaripuh way-seputih | N/A | 2007 |
| Allomogurnda sampricei | Eleotridae | Bekut-sungai malaa | 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 |