| Order |
Clade |
Family |
Genus |
Species |
Synonyms |
Image |
Age |
| †Cimolesta | †Pantodonta | †Coryphodontidae | | †Coryphodontidae sp.[8] | | | Early–Middle Eocene |
| †Asiocoryphodon [es] | †Asiocoryphodon sp.[8] | | |
| †Tillodontia | †Esthonychidae [ru] | †Trogosus | †Trogosus cf. T. latidens[8] | | |
| †Higotherium | †H. hypsodon Miyata & Tomida, 1998[9] | | | Middle Eocene |
| Proboscidea | †Gomphotherioidea | †Gomphotheriidae | †Gomphotherium | †G. annectens [species] | Hemimastodon annectens Matsumoto, 1924[10] |  | Early Miocene |
Bunolophodon yokotii Makiyama, 1938[11] |
| †Sinomastodon | †S. sendaicus [it][12] | Trilophodon sendaicus Matsumoto, 1924[10] | | Early Pliocene |
| Elephantoidea | †Stegodontidae | †Stegolophodon | †S. pseudolatidens[13] | Eostegodon pseudolatidens Yabe, 1950[14] |  | Miocene |
Stegolophodon tsudai Shikama & Kirii, 1956[15] |
Stegolophodon miyokoae Hatai, 1959[16] |
| †Stegodon | †S. miensis [ja] | Stegodon clifti miensis Matsumoto, 1941[17] |  | Pliocene |
Stegolophodon shinshuensis Fossil Elephant Research Group, 1979[18] |
Stegodon bombifrons Itsukaichi Stegodon Research Group, 1980[19] |
| Stegodon cf. elephantoides[20] |
†S. protoaurorae [ja] Aiba, Baba & Matsukawa, 2010[21] | | | Late Pliocene–Early Pleistocene |
| †S. aurorae[20] | Elephas aurorae Matsumoto, 1918[22] |  | Early Pleistocene |
Parastegodon? kwantoensis Tokunaga, 1934[23] |
Parastegodon sugiyamai Tokunaga, 1935[24] |
Parastegodon akashiensis Takai, 1936[25] |
Parastegodon infrequens Shikama, 1937[26] |
| Stegodon shodoensis (partim)[20] |
| †S. orientalis[20][27] | Stegodon orientalis shodoensis Matsumoto, 1924[28] |  | Middle Pleistocene |
| Elephantidae | †Palaeoloxodon | †P. naumanni[11][29]: 86 | Elephas namadicus naumanni Makiyama, 1924[30] |  | Middle–Late Pleistocene |
Loxodonta (Palaeoloxodon) tokunagai Matsumoto, 1924[31] |
Elephas indicus buski Matsumoto, 1927[32] |
Loxodonta (Palaeoloxodon) namadica yabei Matsumoto, 1929[33] |
Palaeoloxodon yokohamanus Tokunaga, 1934[34] |
Palaeoloxodon aomoriensis Tokunaga & Takai, 1936[35] |
Elephas (Palaeoloxodon) namadicus setoensis Makiyama, 1929[36] |
| †Mammuthus | †M. trogontherii[37]: 347 [38] | Euelephas protomammonteus Matsumoto, 1924[39] |  | Early Pleistocene |
Parelephas protomammonteus proximus Matsumoto, 1926[40] |
Parelephas protomammonteus typicus Matsumoto, 1926[40] |
Elephas primigenius matsumotoi Dietrich, 1927[41] |
Parelephas proximus uehataensis Shikama, 1937[42] |
Archidiskodon paramammonteus shigensis Matsumoto & Ozaki, 1959[43] |
| †M. primigenius[44] | |  | Late Pleistocene |
| Sirenia | | Dugongidae | †Dusisiren | †D. dewana [species] Takahashi, Domning & Saito, 1986[45] | | | Late Miocene |
†D. takasatensis [species] Kobayashi, Horikawa & Miyazaki, 1995[46] | | |
| †Hydrodamalis | †H. spissa Furusawa, 1988[47] | | | Late Pliocene |
| Lagomorpha | | Ochotonidae | †Alloptox [es] | †A. japonicus Tomida, 2012[48] | |  | Early Miocene |
| Rodentia | Hystricomorpha | | | Ctenodactyloidea sp.[8] | | | Early–Middle Eocene |
| Diatomyidae | †Diatomys | †D. shantungensis[49][50] | | | Early Miocene |
| Castorimorpha | Castoridae | †Steneofiber | †Steneofiber sp.[49] | | | Late Oligocene |
| †Youngofiber | †Y. sinensis[51] | Trogontherium sinensis Young, 1955[52] | | Early Miocene |
| †Minocastor | †M. godai Mörs, Tomida & Kalthoff, 2016[53] | | |
| †Euroxenomys | †E. nanus Mörs & Tomida, 2018[54] | | |
| †Eomyoidea | †Eomyidae | †Megapeomys | †M. repenningi Tomida, 2011[55] | | | Early Miocene |
| †Japaneomys | †J. yasunoi Kimura et al., 2019[56] | | |
| Myomorpha | Cricetidae | Microtus | †M. epiratticepoides Kawamura, 1988[57] | | | Middle–Late Pleistocene |
| Clethrionomys | †C. japonicus Kawamura, 1988[57] | | | Middle Pleistocene |
| Cricetulus | Cricetulus sp.[58] | | |
| Muridae | Niviventer | Niviventer sp.[59] | | | Late Pleistocene-Holocene |
| Rattus | †R. miyakoensis Kawaguchi, Kaneko & Hasegawa, 2009[60] | | | Late Pleistocene |
| Primates | Haplorhini | Cercopithecidae | †Kanagawapithecus | †K. leptopostorbitalis [species] | Dolichopithecus (Kanagawapithecus) leptopostorbitalis Iwamoto, Hasegawa & Koizumi, 2005[61] | | Pliocene |
| Strepsirrhini | †Sivaladapidae | | †Sivaladapidae sp.[8] | | | Early–Middle Eocene |
| Eulipotyphla | | †Plesiosoricidae [pt] | †Plesiosorex [it] | †P. fejfari Oshima, Tomida & Orihara, 2017[62] | | | Early Miocene |
| Soricidae | †Shikamainosorex | †S. densicingulata [species] Hasegawa, 1957[63] | | | Middle Pleistocene |
| Anourosorex | †A. japonicus Shikama & Hasegawa, 1958[64] | | | Late Pleistocene |
| Chiroptera | Yangochiroptera | Vespertilionidae | †Pleistomyotis | †P. longihumeralis[65][58] | | | Middle Pleistocene |
| Myotis | †M. okafujii[58] | | |
| †M. beppuensis[58] | | |
| †Desmostylia | | | †Behemotops | †B. katsuiei Inuzuka, 2000[66] | | | Late Oligocene |
| †Desmostylidae | †Ashoroa | †A. laticosta Inuzuka, 2000[66] | |  |
| †Desmostylus | †D. japonicus Tokunaga & Iwasaki, 1914[67][68] | |  | Miocene |
| †Paleoparadoxiidae | †Paleoparadoxia | †P. tabatai | Cornwallius tabatai Tokunaga, 1939[69] |  |
†P. media Inuzuka, 2005[70] | | |
| Artiodactyla | Suina | Suidae | | Suidae indet.[50] | Palaeochoerus japonicus Takai, 1954[71] | | Early Miocene |
| †Hyotherium | †H. shanwangense[72] | | | Middle Miocene |
| Cetancodontamorpha | †Entelodontidae | †Entelodon | †E. gobiensis[73] | | | Late Eocene |
| | †Dichobunoidea sp.[8] | | | Middle–Late Eocene |
| †Anthracotheriidae | †Bothriogenys | †Bothriogenys sp.[73] | | | Late Eocene |
| †Bothriodon | †B. sandaensis Tsubamoto et al., 2007[74] | | | Middle–Late Eocene |
| †Elomeryx | †E. japonicus[75] | Brachyodus japonicus Matsumoto, 1925[76] |  | Middle Oligocene |
| Cetacea | | †Sinanodelphis | †S. izumidaensis [species] Makiyama, 1936[77] | | | Miocene |
| Delphinidae | †Eodelphinus | †E. kabatensis | Stenella kabatensis Horikawa, 1977[78] | |
| †Norisdelphis | †N. annakaensis [uk] Kimura & Hasegawa, 2020[79] | | |
| Pseudorca | †P. yokoyamai Matsumoto, 1926[80] | | | Pliocene |
| Orcinus | †O. paleorca | Orca paleorca Matsumoto, 1937[81] | | Early Pleistocene |
| †Kentriodontidae | †Kentriodon | †K. sugawarai [species] Guo & Kohno, 2021[82] | | | Early–Middle Miocene |
†K. hobetsu [species] Ichishima, 1994[83] | | | Middle Miocene |
| Monodontidae | †Haborodelphis | †H. japonicus [species] Ichishima et al., 2018[84] | | | Early Pliocene |
| Phocoenidae | †Miophocaena | †M. nishinoi Murakami et al., 2012[85] | | | Late Miocene |
| †Archaeophocaena | †A. teshioensis Murakami et al., 2012[85] | | |
| †Pterophocaena | †P. nishinoi Murakami et al., 2012[86] | | |
| †Haborophocoena | †H. toyoshimai [species] Ichishima & Kimura, 2005[87] | | | Early Pliocene |
†H. minutus [species] Ichishima & Kimura, 2009[88] | | |
| †Numataphocoena | †N. yamashitai [species] Ichishima & Kimura, 2000[89] | | |
| Ziphiidae | Berardius | †B. kobayashii Kawatani & Kohno, 2021[90] | | | Middle–Late Miocene |
| †Allodelphinidae | †Ninjadelphis | †N. ujiharai [species] Kimura & Barnes, 2016[91] | | | Early Miocene |
| †Awadelphis | †A. hirayamai Murakami, 2016[92] | | | Late Miocene |
| †Miophyseter | †M. chitaensis Kimura & Hasegawa, 2022[93] | | | Early Miocene |
| †Brygmophyseter | †B. shigensis | Scaldicetus shigensis Hirota & Barnes, 1994[94] |  | Middle Miocene |
| †Eomysticetidae | †Yamatocetus | †Y. canaliculatus Okazaki, 2012[95] | | | Late Oligocene |
| Balaenidae | †Idiocetus | †I. tsugarensis Matsumoto, 1926[80] | | | Late Miocene |
| †Archaeobalaena | †A. dosanko [species] Tanaka, Furusawa & Kimura, 2020[96] | | | Early Pliocene |
| †Taikicetus | †T. inouei Tanaka, Ando & Sawamura, 2018[97] | | | Middle Miocene |
| †Isanacetus | †I. laticephalus [species] Kimura & Ozawa, 2002[98] | | | Early Miocene |
| †Diorocetus | †D. chichibuensis [ja] Yoshida, Kimura & Hasegawa, 2003[99] | | | Miocene |
†D. shobarensis [ja] Otsuka & Ota, 2008[100] | | | Middle Miocene |
| †Parietobalaena | †P. yamaokai [species] Otsuka & Ota, 2008[100] | | |
| Cetotheriidae | †Hibacetus | †H. hirosei [species] Otsuka & Ota, 2008[100] | | |
| †Joumocetus | †J. shimizui Kimura & Hasegawa, 2010[101] | | | Late Miocene |
| Balaenopteridae | Eschrichtius | †E. akishimaensis Kimura, Hasegawa & Kohno, 2018[102] | | | Early Pleistocene |
| Ruminantia | | | Cervoidea indet.[50] | Amphitragulus minoensis Matsumoto, 1918[103] | | Early Miocene |
| Cervidae | †Dicrocerus | †D. tokunagai Matsumoto, 1927[104][105] | | |
| †Cervavus | †C. oweni hirabayashii Tokunaga, 1926[106][105] | | | Late Miocene |
| †Metaplatyceros | †M. sequoiae Shikama, 1941[107] | | | Late Pliocene |
| Axis | †A. japonicus[108] | Cervus (Axis) japonicus Otsuka, 1967[109] | | Early Pleistocene |
| Axis kyushuensis[110] |
| Elaphurus | †E. akashiensis | Cervus akasiensis Shikama, 1941[107] | | Late Pliocene |
| †E. bifurcatus shikamai[111] | Elaphurus shikamai [ja] Otsuka, 1968[112] | | Early Pleistocene |
| †E. davidianus tamaensis[111] | Elaphurus (Elaphurus) tamaensis Shikama & Hasegawa, 1976[113] | |
| †E. davidianus menziesianus[111] | Capreolus (Capreolina) mayai Tokunaga & Takai, 1936[114] | | Middle–Late Pleistocene |
| Elaphurus mayai[115] |
| Cervus | †C. (Nipponicervus) kazusensis[116][108] | Cervus (Sika) kazusensis Matsumoto, 1926[117] | | Pleistocene |
Cervus (Deperetia) trassaerti Shikama, 1941[107] |
Cervus (Deperetia) urbanus Shikama, 1941[107] |
Cervus (Anoglochis) praenipponicus [ja] Shikama, 1936[118] |
Cervus (Deperetia) naorai Shikama, 1936[119] |
Cervus (Nipponicervus?) takaoi Otsuka & Shikama, 1977[120] |
Cervus (Deperetia) shimabarensis Otsuka, 1967[109] |
| †C. astylodon | Muntiacus astylodon Matsumoto, 1926[117] |  |
Cervus (Rucervus) riukiuensis Matsumoto, 1926[117] |
| †C. greyi katokiyomasai[121][122] | Cervus (Rucervus) katokiyomasai Shikama & Hasegawa, 1965[123] | |
Cervus (Sika) natsumei Matsumoto, 1938[124] |
Cervus (Sika) paleoezoensis Otsuka & Shikama, 1977[120] |
| †C. kyushuensis | Cervus (Rusa) kyushuensis Otsuka, 1966[125] | | Early Pleistocene |
| †C. akiyoshiensis | Cervus (Nipponicervus) akiyoshiensis Otsuka, 1977[126] | | Late Pleistocene |
| †Sinomegaceros | †S. yabei [ja][120] | Cervus (Sinomegaceros) yabei Shikama, 1938[127] |  | Pleistocene |
Megaceros kinryuensis Matsumoto & Mori, 1956[128] |
Megaceros (Sinomegaceros) ordosianus minor Kamei, 1958[129] |
Giraffa (Orasius?) nipponica Matsumoto, 1926[117][130] |
| Capreolus | †C. tokunagai [species] Otuka, 1941[131] | Capreolus miyakoensis Hasegawa, Otsuka & Nohara, 1973[132] | | Pleistocene–Holocene |
| Bovidae | Bubalus | Bubalus sp.[58] | | | Middle Pleistocene |
| Bison | †B. hanaizumiensis [species] | Leptobison hanaizumiensis Matsumoto & Mori, 1956[128] |  | Late Pleistocene |
| †B. priscus[58] | | |
| Capricornis | †C. (?) nikitini[116] | Naemorhedus nikitini Shikama, 1949[133] | | Pleistocene |
| Perissodactyla | | †Hyopsodontidae | †Hyopsodus | †Hyopsodus sp.[8] | | | Early–Middle Eocene |
| Hippomorpha | †Brontotheriidae | | †Brontotheriidae sp.[8] | | |
| Equidae | †Anchitherium | †Anchitherium aff. A. gobiense[134] | Anchitherium hypohippoides Matsumoto, 1921[135] | | Early Miocene |
| †Ancylopoda | †Isectolophidae | †Isectolophus [it] | †Isectolophus sp.[8] | | | Early–Middle Eocene |
| †Chalicotheriidae | | †Schizotheriinae sp.[136] | | | Early Miocene |
| Tapiroidea | †Helaletidae | †Plesiocolopirus | †P. grangeri[8] | Desmatotherium grangeri Tokunaga, 1933[137] | | Middle Eocene |
| †P. kushiroensis [ja] | Colodon kushiroensis Tomida, 1983[138] | | Middle Eocene–Early Oligocene |
| Tapiridae | †Plesiotapirus | †P. yagii [species] | Palaeotapirus yagii Matsumoto, 1921[135] |  | Early Miocene |
| Rhinocerotoidea | †Hyrachyidae [nl] | †Hyrachyus | cf. †Hyrachyus sp.[74] | | | Early–Middle Eocene |
| †Amynodontidae | †Zaisanamynodon | †Zaisanamynodon cf. Z. protheroi[8] | | | Middle–Late Eocene |
| cf. †Z. borisovi[8] | | | Late Eocene |
| †Amynodon [it] | †A. watanabei[8] | †Amynodon (?) watanabei Tokunaga, 1926[139] | | Middle–Late Eocene |
| Rhinocerotidae | †Brachypotherium | †B. pugnator[136] | Teleoceras (Brachypotherium) pugnator Matsumoto, 1921[135] |  | Early Miocene |
| Chilotherium pugnator |
Teleoceras (?) kaniensis Tokunaga, 1926[139] |
Teleoceras (?) tokiensis Tokunaga, 1926[139] |
| †Plesiaceratherium | †Plesiaceratherium sp.[50] | | |
| †Stephanorhinus | †S. kirchbergensis[140] | Dicerorhinus nipponicus [ja] Shikama, 1967[141] |  | Middle Pleistocene |
Rhinoceros shindoi Tokunaga, 1931[142] |
| Carnivora | | †Miacidae | | †Miacidae sp.[8] | | | Early–Middle Eocene |
| Feliformia | Felidae | Panthera | †P. youngi[143] | Felis youngi | | Middle Pleistocene |
| Felis | †F. microtus[144] | | | Pleistocene |
| †Amphicyonoidea | †Amphicyonidae | †Ysengrinia | †Ysengrinia sp.[145] | | | Middle Miocene |
| Canoidea | Canidae | Canis | †C. falconeri[146] | | | Early Pleistocene |
| Cuon | Cuon sp.[147] | | | Middle Pleistocene |
| Nyctereutes | †N. viverrinus nipponicus Shikama, 1949[133] | | | Pleistocene |
| Musteloidea | Ailuridae | †Parailurus | †Parailurus sp.[148] | | | Early–Middle Pliocene |
| Mustelidae | Meles | †M. mukasianakuma Shikama, 1949[133][58] | | | Middle Pleistocene |
†M. leucurus kuzuuensis Shikama, 1949[133][58] | | |
| Martes | †M. ten [species] Shikama, 1949[133] | | | Pleistocene |
| †Enhydrictis | †E. (Oriensictis) nipponica | Lutra nipponica Naora, 1968[149] | | Middle Pleistocene |
| Oriensictis nipponica[150] |
| Mustela | †M. constricta[58][144] | | |
| †M. kuzuuensis[58] | Putorius kuzuuensis Shikama, 1949[133] | | Late Pleistocene |
| Pinnipedia[151] | †Desmatophocidae | †Allodesmus[152] | †A. uraiporensis [species] Tonomori et al., 2018[152] | |  | Middle Miocene |
†A. naorai [species] Kohno, 1996[153] | | |
| †A. sinanoensis[153] | Eumetopias sinanoensis Nagao, 1941[154] |  |
| Megagomphos sinanoensis[155] |
Allodesmus megallos Hirota, 1995[155] |
Allodesmus sadoensis Hirota, 1995[155] |
| †Allodesmus sp.[156] | |  |
| Otariidae | †Thalassoleon | †T. inouei Kohno, 1992[157] | | | Pliocene |
| †Oriensarctos | †O. watasei [species] | Eumetopias watasei Matsumoto, 1925[158] | | Early Pleistocene |
| Callorhinus | †C. gilmorei[159] | | | Pliocene |
| Otariidae sp. | Eumetopias ojiyaensis [species] Horikawa, 1981[160] | | Late Pleistocene |
| Odobenidae | †Prototaria | †P. planicephala Kohno, 1994[161] | | | Middle Miocene |
†P. primigena Takeyama & Ozawa, 1984[162] | | |
| †Pseudotaria | †P. muramotoi [species] Kohno, 2006[163] | | | Miocene |
| †Archaeodobenus | †A. akamatsui Tanaka & Kohno, 2015[164] | |  | Late Miocene |
| †Protodobenus | †P. japonicus [species] Horikawa, 1995[165] | | | Early Pliocene |
| Odobenus | †O. mandanoensis [species] Tomida, 1989[166] | | | Middle Pleistocene |