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

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

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

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

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

Order: Petromyzontiformes

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

Order: Acipenseriformes

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

Order: Anguilliformes

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

Order: Atheriniformes Family: Atherinidae Genus: Atherinomorus , Atherinomorus duodecimalis (MoE: DD) Genus: Hypoatherina , Hypoatherina temminckii (MoE: DD) Family: Atherinopsidae Genus: Odontesthes Argentinian silverside, Odontesthes bonariensis(introduced)

Order: Aulopiformes Family: Synodontidae Genus: Saurida Clouded lizardfish, Saurida nebulosa

Order: Beloniformes

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

Order: Callionymiformes Family: Callionymidae Genus: Pseudocalliurichthys , Pseudocalliurichthys ikedai(MoE: DD)

Order: Clupeiformes

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

Order: Cypriniformes

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

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

Order: Elopiformes

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