# List of prehistoric mammals of Japan

This list is of prehistoric mammalsdon't move to "fossil mammals" because many/most of the extant mammals of Japan are also known from the (sub)fossil record known from the fossil record of the Japanese archipelago. For extant mammals from the area, see List of mammals of Japan (which includes the recently extinct species on the IUCN Red List and its domestic counterpart the Ministry of the Environment Red List). Other species that have gone extinct in historic times and extant species that have been locally extirpated and no longer form part of the fauna of Japan but are known from the fossil or subfossil record are additionally listed at the bottom of this page.

## Mesozoic

| Clade | Order | Family | Genus | Species | Horizon | Age |
| Trechnotheria | †"Symmetrodonta" | †Spalacotheriidae | †Symmetrolestes | †S. parvus Tsubamoto & Rougier, 2004 | Kitadani Formation | Early Cretaceous |
| Theriimorpha | †Eutriconodonta | †Amphidontidae | †Hakusanodon | †H. archaeus Rougier et al., 2007 | Kuwajima Formation | Early Cretaceous |
| †Allotheria | †Multituberculata | †Eobaataridae | †Hakusanobaatar | †H. matsuoi Kusuhashi, 2008 | Kuwajima Formation | Early Cretaceous |
| †Allotheria | †Multituberculata | †Eobaataridae | †Tedoribaatar [it] | †T. reini Kusuhashi, 2008 | Kuwajima Formation | Early Cretaceous |
| Eutheria | †Asioryctitheria | | †Sasayamamylos [ja] | †S. kawaii Kusuhashi & Saegusa, 2013 | Sasayama Group | Early Cretaceous |
| Eutheria | | †Zhelestidae | †Sorlestes | †S. mifunensis Setoguchi et al., 1999 | Mifune Group | Late Cretaceous |

## Cenozoic

| Order | Clade | Family | Genus | Species | Synonyms | Age |
| †Cimolesta | †Pantodonta | †Coryphodontidae | | †Coryphodontidae sp. | | Early–Middle Eocene |
| †Cimolesta | †Pantodonta | †Coryphodontidae | †Asiocoryphodon [es] | †Asiocoryphodon sp. | | Early–Middle Eocene |
| †Cimolesta | †Tillodontia | †Esthonychidae [ru] | †Trogosus | †Trogosus cf. T. latidens | | Early–Middle Eocene |
| †Cimolesta | †Tillodontia | †Esthonychidae [ru] | †Higotherium | †H. hypsodon Miyata & Tomida, 1998 | | Middle Eocene |
| Proboscidea | †Gomphotherioidea | †Gomphotheriidae | †Gomphotherium | †G. annectens [species] | Hemimastodon annectens Matsumoto, 1924 | Early Miocene |
| Proboscidea | †Gomphotherioidea | †Gomphotheriidae | †Gomphotherium | †G. annectens [species] | Bunolophodon yokotii Makiyama, 1938 | Early Miocene |
| Proboscidea | †Gomphotherioidea | †Gomphotheriidae | †Sinomastodon | †S. sendaicus [it] | Trilophodon sendaicus Matsumoto, 1924 | Early Pliocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegolophodon | †S. pseudolatidens | Eostegodon pseudolatidens Yabe, 1950 | Miocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegolophodon | †S. pseudolatidens | Stegolophodon tsudai Shikama & Kirii, 1956 | Miocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegolophodon | †S. pseudolatidens | Stegolophodon miyokoae Hatai, 1959 | Miocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. miensis [ja] | Stegodon clifti miensis Matsumoto, 1941 | Pliocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. miensis [ja] | Stegolophodon shinshuensis Fossil Elephant Research Group, 1979 | Pliocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. miensis [ja] | Stegodon bombifrons Itsukaichi Stegodon Research Group, 1980 | Pliocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. miensis [ja] | Stegodon cf. elephantoides | Pliocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. protoaurorae [ja] Aiba, Baba & Matsukawa, 2010 | | Late Pliocene–Early Pleistocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. aurorae | Elephas aurorae Matsumoto, 1918 | Early Pleistocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. aurorae | Parastegodon? kwantoensis Tokunaga, 1934 | Early Pleistocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. aurorae | Parastegodon sugiyamai Tokunaga, 1935 | Early Pleistocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. aurorae | Parastegodon akashiensis Takai, 1936 | Early Pleistocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. aurorae | Parastegodon infrequens Shikama, 1937 | Early Pleistocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. aurorae | Stegodon shodoensis (partim) | Early Pleistocene |
| Proboscidea | Elephantoidea | †Stegodontidae | †Stegodon | †S. orientalis | Stegodon orientalis shodoensis Matsumoto, 1924 | Middle Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Palaeoloxodon | †P. naumanni$^{:86}$ | Elephas namadicus naumanni Makiyama, 1924 | Middle–Late Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Palaeoloxodon | †P. naumanni$^{:86}$ | Loxodonta (Palaeoloxodon) tokunagai Matsumoto, 1924 | Middle–Late Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Palaeoloxodon | †P. naumanni$^{:86}$ | Elephas indicus buski Matsumoto, 1927 | Middle–Late Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Palaeoloxodon | †P. naumanni$^{:86}$ | Loxodonta (Palaeoloxodon) namadica yabei Matsumoto, 1929 | Middle–Late Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Palaeoloxodon | †P. naumanni$^{:86}$ | Palaeoloxodon yokohamanus Tokunaga, 1934 | Middle–Late Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Palaeoloxodon | †P. naumanni$^{:86}$ | Palaeoloxodon aomoriensis Tokunaga & Takai, 1936 | Middle–Late Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Palaeoloxodon | †P. naumanni$^{:86}$ | Elephas (Palaeoloxodon) namadicus setoensis Makiyama, 1929 | Middle–Late Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Mammuthus | †M. trogontherii$^{:347}$ | Euelephas protomammonteus Matsumoto, 1924 | Early Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Mammuthus | †M. trogontherii$^{:347}$ | Parelephas protomammonteus proximus Matsumoto, 1926 | Early Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Mammuthus | †M. trogontherii$^{:347}$ | Parelephas protomammonteus typicus Matsumoto, 1926 | Early Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Mammuthus | †M. trogontherii$^{:347}$ | Elephas primigenius matsumotoi Dietrich, 1927 | Early Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Mammuthus | †M. trogontherii$^{:347}$ | Parelephas proximus uehataensis Shikama, 1937 | Early Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Mammuthus | †M. trogontherii$^{:347}$ | Archidiskodon paramammonteus shigensis Matsumoto & Ozaki, 1959 | Early Pleistocene |
| Proboscidea | Elephantoidea | Elephantidae | †Mammuthus | †M. primigenius | | Late Pleistocene |
| Sirenia | | Dugongidae | †Dusisiren | †D. dewana [species] Takahashi, Domning & Saito, 1986 | | Late Miocene |
| Sirenia | | Dugongidae | †Dusisiren | †D. takasatensis [species] Kobayashi, Horikawa & Miyazaki, 1995 | | Late Miocene |
| Sirenia | | Dugongidae | †Hydrodamalis | †H. spissa Furusawa, 1988 | | Late Pliocene |
| Lagomorpha | | Ochotonidae | †Alloptox [es] | †A. japonicus Tomida, 2012 | | Early Miocene |
| Rodentia | Hystricomorpha | | | Ctenodactyloidea sp. | | Early–Middle Eocene |
| Rodentia | Hystricomorpha | Diatomyidae | †Diatomys | †D. shantungensis | | Early Miocene |
| Rodentia | Castorimorpha | Castoridae | †Steneofiber | †Steneofiber sp. | | Late Oligocene |
| Rodentia | Castorimorpha | Castoridae | †Youngofiber | †Y. sinensis | Trogontherium sinensis Young, 1955 | Early Miocene |
| Rodentia | Castorimorpha | Castoridae | †Minocastor | †M. godai Mörs, Tomida & Kalthoff, 2016 | | Early Miocene |
| Rodentia | Castorimorpha | Castoridae | †Euroxenomys | †E. nanus Mörs & Tomida, 2018 | | Early Miocene |
| Rodentia | †Eomyoidea | †Eomyidae | †Megapeomys | †M. repenningi Tomida, 2011 | | Early Miocene |
| Rodentia | †Eomyoidea | †Eomyidae | †Japaneomys | †J. yasunoi Kimura et al., 2019 | | Early Miocene |
| Rodentia | Myomorpha | Cricetidae | Microtus | †M. epiratticepoides Kawamura, 1988 | | Middle–Late Pleistocene |
| Rodentia | Myomorpha | Cricetidae | Clethrionomys | †C. japonicus Kawamura, 1988 | | Middle Pleistocene |
| Rodentia | Myomorpha | Cricetidae | Cricetulus | Cricetulus sp. | | Middle Pleistocene |
| Rodentia | Myomorpha | Muridae | Niviventer | Niviventer sp. | | Late Pleistocene-Holocene |
| Rodentia | Myomorpha | Muridae | Rattus | †R. miyakoensis Kawaguchi, Kaneko & Hasegawa, 2009 | | Late Pleistocene |
| Primates | Haplorhini | Cercopithecidae | †Kanagawapithecus | †K. leptopostorbitalis [species] | Dolichopithecus (Kanagawapithecus) leptopostorbitalis Iwamoto, Hasegawa & Koizumi, 2005 | Pliocene |
| Primates | Strepsirrhini | †Sivaladapidae | | †Sivaladapidae sp. | | Early–Middle Eocene |
| Eulipotyphla | | †Plesiosoricidae [pt] | †Plesiosorex [it] | †P. fejfari Oshima, Tomida & Orihara, 2017 | | Early Miocene |
| Eulipotyphla | | Soricidae | †Shikamainosorex | †S. densicingulata [species] Hasegawa, 1957 | | Middle Pleistocene |
| Eulipotyphla | | Soricidae | Anourosorex | †A. japonicus Shikama & Hasegawa, 1958 | | Late Pleistocene |
| Chiroptera | Yangochiroptera | Vespertilionidae | †Pleistomyotis | †P. longihumeralis | | Middle Pleistocene |
| Chiroptera | Yangochiroptera | Vespertilionidae | Myotis | †M. okafujii | | Middle Pleistocene |
| Chiroptera | Yangochiroptera | Vespertilionidae | Myotis | †M. beppuensis | | Middle Pleistocene |
| †Desmostylia | | | †Behemotops | †B. katsuiei Inuzuka, 2000 | | Late Oligocene |
| †Desmostylia | | †Desmostylidae | †Ashoroa | †A. laticosta Inuzuka, 2000 | | Late Oligocene |
| †Desmostylia | | †Desmostylidae | †Desmostylus | †D. japonicus Tokunaga & Iwasaki, 1914 | | Miocene |
| †Desmostylia | | †Paleoparadoxiidae | †Paleoparadoxia | †P. tabatai | Cornwallius tabatai Tokunaga, 1939 | Miocene |
| †Desmostylia | | †Paleoparadoxiidae | †Paleoparadoxia | †P. media Inuzuka, 2005 | | Miocene |
| Artiodactyla | Suina | Suidae | | Suidae indet. | Palaeochoerus japonicus Takai, 1954 | Early Miocene |
| Artiodactyla | Suina | Suidae | †Hyotherium | †H. shanwangense | | Middle Miocene |
| Artiodactyla | Cetancodontamorpha | †Entelodontidae | †Entelodon | †E. gobiensis | | Late Eocene |
| Artiodactyla | Cetancodontamorpha | | | †Dichobunoidea sp. | | Middle–Late Eocene |
| Artiodactyla | Cetancodontamorpha | †Anthracotheriidae | †Bothriogenys | †Bothriogenys sp. | | Late Eocene |
| Artiodactyla | Cetancodontamorpha | †Anthracotheriidae | †Bothriodon | †B. sandaensis Tsubamoto et al., 2007 | | Middle–Late Eocene |
| Artiodactyla | Cetancodontamorpha | †Anthracotheriidae | †Elomeryx | †E. japonicus | Brachyodus japonicus Matsumoto, 1925 | Middle Oligocene |
| Artiodactyla | Cetacea | | †Sinanodelphis | †S. izumidaensis [species] Makiyama, 1936 | | Miocene |
| Artiodactyla | Cetacea | Delphinidae | †Eodelphinus | †E. kabatensis | Stenella kabatensis Horikawa, 1977 | Miocene |
| Artiodactyla | Cetacea | Delphinidae | †Norisdelphis | †N. annakaensis [uk] Kimura & Hasegawa, 2020 | | Miocene |
| Artiodactyla | Cetacea | Delphinidae | Pseudorca | †P. yokoyamai Matsumoto, 1926 | | Pliocene |
| Artiodactyla | Cetacea | Delphinidae | Orcinus | †O. paleorca | Orca paleorca Matsumoto, 1937 | Early Pleistocene |
| Artiodactyla | Cetacea | †Kentriodontidae | †Kentriodon | †K. sugawarai [species] Guo & Kohno, 2021 | | Early–Middle Miocene |
| Artiodactyla | Cetacea | †Kentriodontidae | †Kentriodon | †K. hobetsu [species] Ichishima, 1994 | | Middle Miocene |
| Artiodactyla | Cetacea | Monodontidae | †Haborodelphis | †H. japonicus [species] Ichishima et al., 2018 | | Early Pliocene |
| Artiodactyla | Cetacea | Phocoenidae | †Miophocaena | †M. nishinoi Murakami et al., 2012 | | Late Miocene |
| Artiodactyla | Cetacea | Phocoenidae | †Archaeophocaena | †A. teshioensis Murakami et al., 2012 | | Late Miocene |
| Artiodactyla | Cetacea | Phocoenidae | †Pterophocaena | †P. nishinoi Murakami et al., 2012 | | Late Miocene |
| Artiodactyla | Cetacea | Phocoenidae | †Haborophocoena | †H. toyoshimai [species] Ichishima & Kimura, 2005 | | Early Pliocene |
| Artiodactyla | Cetacea | Phocoenidae | †Haborophocoena | †H. minutus [species] Ichishima & Kimura, 2009 | | Early Pliocene |
| Artiodactyla | Cetacea | Phocoenidae | †Numataphocoena | †N. yamashitai [species] Ichishima & Kimura, 2000 | | Early Pliocene |
| Artiodactyla | Cetacea | Ziphiidae | Berardius | †B. kobayashii Kawatani & Kohno, 2021 | | Middle–Late Miocene |
| Artiodactyla | Cetacea | †Allodelphinidae | †Ninjadelphis | †N. ujiharai [species] Kimura & Barnes, 2016 | | Early Miocene |
| Artiodactyla | Cetacea | | †Awadelphis | †A. hirayamai Murakami, 2016 | | Late Miocene |
| Artiodactyla | Cetacea | | †Miophyseter | †M. chitaensis Kimura & Hasegawa, 2022 | | Early Miocene |
| Artiodactyla | Cetacea | | †Brygmophyseter | †B. shigensis | Scaldicetus shigensis Hirota & Barnes, 1994 | Middle Miocene |
| Artiodactyla | Cetacea | †Eomysticetidae | †Yamatocetus | †Y. canaliculatus Okazaki, 2012 | | Late Oligocene |
| Artiodactyla | Cetacea | Balaenidae | †Idiocetus | †I. tsugarensis Matsumoto, 1926 | | Late Miocene |
| Artiodactyla | Cetacea | Balaenidae | †Archaeobalaena | †A. dosanko [species] Tanaka, Furusawa & Kimura, 2020 | | Early Pliocene |
| Artiodactyla | Cetacea | | †Taikicetus | †T. inouei Tanaka, Ando & Sawamura, 2018 | | Middle Miocene |
| Artiodactyla | Cetacea | | †Isanacetus | †I. laticephalus [species] Kimura & Ozawa, 2002 | | Early Miocene |
| Artiodactyla | Cetacea | | †Diorocetus | †D. chichibuensis [ja] Yoshida, Kimura & Hasegawa, 2003 | | Miocene |
| Artiodactyla | Cetacea | | †Diorocetus | †D. shobarensis [ja] Otsuka & Ota, 2008 | | Middle Miocene |
| Artiodactyla | Cetacea | | †Parietobalaena | †P. yamaokai [species] Otsuka & Ota, 2008 | | Middle Miocene |
| Artiodactyla | Cetacea | Cetotheriidae | †Hibacetus | †H. hirosei [species] Otsuka & Ota, 2008 | | Middle Miocene |
| Artiodactyla | Cetacea | Cetotheriidae | †Joumocetus | †J. shimizui Kimura & Hasegawa, 2010 | | Late Miocene |
| Artiodactyla | Cetacea | Balaenopteridae | Eschrichtius | †E. akishimaensis Kimura, Hasegawa & Kohno, 2018 | | Early Pleistocene |
| Artiodactyla | Ruminantia | | | Cervoidea indet. | Amphitragulus minoensis Matsumoto, 1918 | Early Miocene |
| Artiodactyla | Ruminantia | Cervidae | †Dicrocerus | †D. tokunagai Matsumoto, 1927 | | Early Miocene |
| Artiodactyla | Ruminantia | Cervidae | †Cervavus | †C. oweni hirabayashii Tokunaga, 1926 | | Late Miocene |
| Artiodactyla | Ruminantia | Cervidae | †Metaplatyceros | †M. sequoiae Shikama, 1941 | | Late Pliocene |
| Artiodactyla | Ruminantia | Cervidae | Axis | †A. japonicus | Cervus (Axis) japonicus Otsuka, 1967 | Early Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Axis | †A. japonicus | Axis kyushuensis | Early Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Elaphurus | †E. akashiensis | Cervus akasiensis Shikama, 1941 | Late Pliocene |
| Artiodactyla | Ruminantia | Cervidae | Elaphurus | †E. bifurcatus shikamai | Elaphurus shikamai [ja] Otsuka, 1968 | Early Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Elaphurus | †E. davidianus tamaensis | Elaphurus (Elaphurus) tamaensis Shikama & Hasegawa, 1976 | Early Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Elaphurus | †E. davidianus menziesianus | Capreolus (Capreolina) mayai Tokunaga & Takai, 1936 | Middle–Late Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Elaphurus | †E. davidianus menziesianus | Elaphurus mayai | Middle–Late Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. (Nipponicervus) kazusensis | Cervus (Sika) kazusensis Matsumoto, 1926 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. (Nipponicervus) kazusensis | Cervus (Deperetia) trassaerti Shikama, 1941 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. (Nipponicervus) kazusensis | Cervus (Deperetia) urbanus Shikama, 1941 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. (Nipponicervus) kazusensis | Cervus (Anoglochis) praenipponicus [ja] Shikama, 1936 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. (Nipponicervus) kazusensis | Cervus (Deperetia) naorai Shikama, 1936 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. (Nipponicervus) kazusensis | Cervus (Nipponicervus?) takaoi Otsuka & Shikama, 1977 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. (Nipponicervus) kazusensis | Cervus (Deperetia) shimabarensis Otsuka, 1967 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. astylodon | Muntiacus astylodon Matsumoto, 1926 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. astylodon | Cervus (Rucervus) riukiuensis Matsumoto, 1926 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. greyi katokiyomasai | Cervus (Rucervus) katokiyomasai Shikama & Hasegawa, 1965 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. greyi katokiyomasai | Cervus (Sika) natsumei Matsumoto, 1938 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. greyi katokiyomasai | Cervus (Sika) paleoezoensis Otsuka & Shikama, 1977 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. kyushuensis | Cervus (Rusa) kyushuensis Otsuka, 1966 | Early Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Cervus | †C. akiyoshiensis | Cervus (Nipponicervus) akiyoshiensis Otsuka, 1977 | Late Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | †Sinomegaceros | †S. yabei [ja] | Cervus (Sinomegaceros) yabei Shikama, 1938 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | †Sinomegaceros | †S. yabei [ja] | Megaceros kinryuensis Matsumoto & Mori, 1956 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | †Sinomegaceros | †S. yabei [ja] | Megaceros (Sinomegaceros) ordosianus minor Kamei, 1958 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | †Sinomegaceros | †S. yabei [ja] | Giraffa (Orasius?) nipponica Matsumoto, 1926 | Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Capreolus | †C. tokunagai [species] Otuka, 1941 | Capreolus miyakoensis Hasegawa, Otsuka & Nohara, 1973 | Pleistocene–Holocene |
| Artiodactyla | Ruminantia | Bovidae | Bubalus | Bubalus sp. | | Middle Pleistocene |
| Artiodactyla | Ruminantia | Bovidae | Bison | †B. hanaizumiensis [species] | Leptobison hanaizumiensis Matsumoto & Mori, 1956 | Late Pleistocene |
| Artiodactyla | Ruminantia | Bovidae | Bison | †B. priscus | | Late Pleistocene |
| Artiodactyla | Ruminantia | Bovidae | Capricornis | †C. (?) nikitini | Naemorhedus nikitini Shikama, 1949 | Pleistocene |
| Perissodactyla | | †Hyopsodontidae | †Hyopsodus | †Hyopsodus sp. | | Early–Middle Eocene |
| Perissodactyla | Hippomorpha | †Brontotheriidae | | †Brontotheriidae sp. | | Early–Middle Eocene |
| Perissodactyla | Hippomorpha | Equidae | †Anchitherium | †Anchitherium aff. A. gobiense | Anchitherium hypohippoides Matsumoto, 1921 | Early Miocene |
| Perissodactyla | †Ancylopoda | †Isectolophidae | †Isectolophus [it] | †Isectolophus sp. | | Early–Middle Eocene |
| Perissodactyla | †Ancylopoda | †Chalicotheriidae | | †Schizotheriinae sp. | | Early Miocene |
| Perissodactyla | Tapiroidea | †Helaletidae | †Plesiocolopirus | †P. grangeri | Desmatotherium grangeri Tokunaga, 1933 | Middle Eocene |
| Perissodactyla | Tapiroidea | †Helaletidae | †Plesiocolopirus | †P. kushiroensis [ja] | Colodon kushiroensis Tomida, 1983 | Middle Eocene–Early Oligocene |
| Perissodactyla | Tapiroidea | Tapiridae | †Plesiotapirus | †P. yagii [species] | Palaeotapirus yagii Matsumoto, 1921 | Early Miocene |
| Perissodactyla | Rhinocerotoidea | †Hyrachyidae [nl] | †Hyrachyus | cf. †Hyrachyus sp. | | Early–Middle Eocene |
| Perissodactyla | Rhinocerotoidea | †Amynodontidae | †Zaisanamynodon | †Zaisanamynodon cf. Z. protheroi | | Middle–Late Eocene |
| Perissodactyla | Rhinocerotoidea | †Amynodontidae | †Zaisanamynodon | cf. †Z. borisovi | | Late Eocene |
| Perissodactyla | Rhinocerotoidea | †Amynodontidae | †Amynodon [it] | †A. watanabei | †Amynodon (?) watanabei Tokunaga, 1926 | Middle–Late Eocene |
| Perissodactyla | Rhinocerotoidea | Rhinocerotidae | †Brachypotherium | †B. pugnator | Teleoceras (Brachypotherium) pugnator Matsumoto, 1921 | Early Miocene |
| Perissodactyla | Rhinocerotoidea | Rhinocerotidae | †Brachypotherium | †B. pugnator | Chilotherium pugnator | Early Miocene |
| Perissodactyla | Rhinocerotoidea | Rhinocerotidae | †Brachypotherium | †B. pugnator | Teleoceras (?) kaniensis Tokunaga, 1926 | Early Miocene |
| Perissodactyla | Rhinocerotoidea | Rhinocerotidae | †Brachypotherium | †B. pugnator | Teleoceras (?) tokiensis Tokunaga, 1926 | Early Miocene |
| Perissodactyla | Rhinocerotoidea | Rhinocerotidae | †Plesiaceratherium | †Plesiaceratherium sp. | | Early Miocene |
| Perissodactyla | Rhinocerotoidea | Rhinocerotidae | †Stephanorhinus | †S. kirchbergensis | Dicerorhinus nipponicus Shikama, 1967 | Middle Pleistocene |
| Perissodactyla | Rhinocerotoidea | Rhinocerotidae | †Stephanorhinus | †S. kirchbergensis | Rhinoceros shindoi Tokunaga, 1931 | Middle Pleistocene |
| Carnivora | | †Miacidae | | †Miacidae sp. | | Early–Middle Eocene |
| Carnivora | Feliformia | Felidae | Panthera | †P. youngi | Felis youngi | Middle Pleistocene |
| Carnivora | Feliformia | Felidae | Felis | †F. microtus | | Pleistocene |
| Carnivora | †Amphicyonoidea | †Amphicyonidae | †Ysengrinia | †Ysengrinia sp. | | Middle Miocene |
| Carnivora | Canoidea | Canidae | Canis | †C. falconeri | | Early Pleistocene |
| Carnivora | Canoidea | Canidae | Cuon | Cuon sp. | | Middle Pleistocene |
| Carnivora | Canoidea | Canidae | Nyctereutes | †N. viverrinus nipponicus Shikama, 1949 | | Pleistocene |
| Carnivora | Musteloidea | Ailuridae | †Parailurus | †Parailurus sp. | | Early–Middle Pliocene |
| Carnivora | Musteloidea | Mustelidae | Meles | †M. mukasianakuma Shikama, 1949 | | Middle Pleistocene |
| Carnivora | Musteloidea | Mustelidae | Meles | †M. leucurus kuzuuensis Shikama, 1949 | | Middle Pleistocene |
| Carnivora | Musteloidea | Mustelidae | Martes | †M. ten [species] Shikama, 1949 | | Pleistocene |
| Carnivora | Musteloidea | Mustelidae | †Enhydrictis | †E. (Oriensictis) nipponica | Lutra nipponica Naora, 1968 | Middle Pleistocene |
| Carnivora | Musteloidea | Mustelidae | †Enhydrictis | †E. (Oriensictis) nipponica | Oriensictis nipponica | Middle Pleistocene |
| Carnivora | Musteloidea | Mustelidae | Mustela | †M. constricta | | Middle Pleistocene |
| Carnivora | Musteloidea | Mustelidae | Mustela | †M. kuzuuensis | Putorius kuzuuensis Shikama, 1949 | Late Pleistocene |
| Carnivora | Pinnipedia | †Desmatophocidae | †Allodesmus | †A. uraiporensis [species] Tonomori et al., 2018 | | Middle Miocene |
| Carnivora | Pinnipedia | †Desmatophocidae | †Allodesmus | †A. naorai [species] Kohno, 1996 | | Middle Miocene |
| Carnivora | Pinnipedia | †Desmatophocidae | †Allodesmus | †A. sinanoensis | Eumetopias sinanoensis Nagao, 1941 | Middle Miocene |
| Carnivora | Pinnipedia | †Desmatophocidae | †Allodesmus | †A. sinanoensis | Megagomphos sinanoensis | Middle Miocene |
| Carnivora | Pinnipedia | †Desmatophocidae | †Allodesmus | †A. sinanoensis | Allodesmus megallos Hirota, 1995 | Middle Miocene |
| Carnivora | Pinnipedia | †Desmatophocidae | †Allodesmus | †A. sinanoensis | Allodesmus sadoensis Hirota, 1995 | Middle Miocene |
| Carnivora | Pinnipedia | †Desmatophocidae | †Allodesmus | †Allodesmus sp. | | Middle Miocene |
| Carnivora | Pinnipedia | Otariidae | †Thalassoleon | †T. inouei Kohno, 1992 | | Pliocene |
| Carnivora | Pinnipedia | Otariidae | †Oriensarctos | †O. watasei [species] | Eumetopias watasei Matsumoto, 1925 | Early Pleistocene |
| Carnivora | Pinnipedia | Otariidae | Callorhinus | †C. gilmorei | | Pliocene |
| Carnivora | Pinnipedia | Otariidae | | Otariidae sp. | Eumetopias ojiyaensis [species] Horikawa, 1981 | Late Pleistocene |
| Carnivora | Pinnipedia | Odobenidae | †Prototaria | †P. planicephala Kohno, 1994 | | Middle Miocene |
| Carnivora | Pinnipedia | Odobenidae | †Prototaria | †P. primigena Takeyama & Ozawa, 1984 | | Middle Miocene |
| Carnivora | Pinnipedia | Odobenidae | †Pseudotaria | †P. muramotoi [species] Kohno, 2006 | | Miocene |
| Carnivora | Pinnipedia | Odobenidae | †Archaeodobenus | †A. akamatsui Tanaka & Kohno, 2015 | | Late Miocene |
| Carnivora | Pinnipedia | Odobenidae | †Protodobenus | †P. japonicus [species] Horikawa, 1995 | | Early Pliocene |
| Carnivora | Pinnipedia | Odobenidae | Odobenus | †O. mandanoensis [species] Tomida, 1989 | | Middle Pleistocene |

## Historical extinctions and local extirpations

| Order | Clade | Family | Genus | Species | Age |
| Sirenia | | Dugongidae | †Hydrodamalis | †H. gigas | Early–Middle Pleistocene |
| Rodentia | Myomorpha | Cricetidae | Microtus | M. oeconomus | Late Pleistocene |
| Rodentia | Myomorpha | Cricetidae | Microtus | M. fortis | Late Pleistocene |
| Rodentia | Myomorpha | Cricetidae | Myopus | M. schisticolor | Middle Pleistocene |
| Artiodactyla | Ruminantia | Cervidae | Rusa | R. unicolor | Pliocene |
| Artiodactyla | Ruminantia | Cervidae | Alces | A. alces | Late Pleistocene |
| Artiodactyla | Ruminantia | Moschidae | Moschus | M. moschiferus | Pleistocene |
| Artiodactyla | Ruminantia | Bovidae | Bos | †B. primigenius | Late Pleistocene |
| Carnivora | Feliformia | Felidae | Panthera | P. pardus | Pleistocene |
| Carnivora | Feliformia | Felidae | Panthera | P. tigris | Pleistocene |
| Carnivora | Feliformia | Felidae | Lynx | L. lynx | Late Pleistocene-Holocene |

## Fossil species synonymized with extant or recently extinct species

| Order | Clade | Family | Genus | Species | Synonyms | Age |
| Artiodactyla | Suinae | Suidae | Sus | S. scrofa | Sus nipponicus Matsumoto, 1915 | Middle–Late Pleistocene |
| Artiodactyla | Suinae | Suidae | Sus | S. scrofa | Sus cf. lydekkeri | Middle–Late Pleistocene |
| Perissodactyla | Hippomorpha | Equidae | Equus | E. caballus | Equus nipponicus Shikama & Onuki, 1962 | Late Pleistocene–Holocene |
| Carnivora | Arctoidea | Ursidae | Ursus | U. arctos | Ursus tanakai Shikama, 1949 | Pleistocene |
| Carnivora | Pinnipedia | Otariidae | Zalophus | Z. californianus$^{:72}$ | Eumetopias (?) kishidai Shikama, 1953 | Pleistocene |
| Carnivora | Pinnipedia | Otariidae | Zalophus | †Z. japonicus$^{:72}$ | Zalophus kimitsensis Matsumoto, 1939 | Early Pleistocene |