| Family | Scientific name | Common name | ||
| Pteropodidae | Pteropus dasymallus Temminck, 1825 | Ryukyu flying fox | inhabits the area from Kuchinoerabu-jima to the Yayeyama Islands | |
| Pteropus loochoensis Gray, 1870 | Okinawa flying fox | extinct | ||
| Pteropus pselaphon Lay, 1829 | Bonin flying fox | endemic to Japan | inhabits the Ogasawara Islands, endemic to Japan | |
| Rhinolophidae | Rhinolophus ferrumequinum Schreber, 1774 | greater horseshoe bat | inhabits the area from Hokkaido to Kyushu | |
| Rhinolophus cornutus Temminck, 1834 | Japanese little horseshoe bat | endemic to Japan | inhabits the area from Hokkaido to Okinoerabu-jima | |
| Rhinolophus pumilus Andersen, 1905 | Okinawa little horseshoe bat | endemic to Japan | inhabits the area from Okinawa-jima to Miyako-jima | |
| Rhinolophus perditus Andersen, 1918 | Yaeyama little horseshoe bat | endemic to Japan | inhabits the Yayeyama Islands | |
| Hipposideridae | Hipposideros turpis Bangs, 1901 | lesser leaf-nosed bat | endemic to Japan | inhabits the Yayeyama Islands |
| Vespertilionidae | Eptesicus japonensis Imaizumi, 1953 | Japanese northern bat | endemic to Japan | inhabits Honshu |
| Eptesicus nilssonii Keyserling & Blasius, 1839 | northern bat | inhabits Hokkaido | ||
| Nyctalus aviator Thomas, 1911 | birdlike noctule | inhabits the area from Hokkaido to Kyushu, abundant in southern Hokkaido and northern and central Honshu. There were also records in Okinawa. | ||
| Nyctalus furvus Imaizumi & Yoshiyuki, 1968 | Japanese noctule | endemic to Japan | was reported from Aomori, Iwate, Fukushima, Tochigi and Nagano | |
| Pipistrellus abramus Temminck, 1840 | Japanese pipistrelle | inhabits the area from Hokkaido to the Yayeyama Islands | ||
| Pipistrellus endoi Imaizumi, 1959 | Endo's pipistrelle | endemic to Japan | inhabits Honshu and Shikoku | |
| Pipistrellus sturdeei Thomas, 1915 | Sturdee's pipistrelle | extinct | ||
| Barbastella darjelingensis Hodgson, 1855 | eastern barbastelle | formerly known as B. leucomelas | inhabits the area from Hokkaido, Honshu, and Shikoku | |
| Plecotus sacrimontis G. M. Allen, 1908 | Japanese long-eared bat | endemic to Japan | inhabits the area from Hokkaido to Kyushu | |
| Hypsugo alaschanicus Bobrinskii, 1926 | Alashanian pipistrelle | has been recorded in Hokkaido, Aomori, and Tsushima | ||
| Vespertilio murinus Linnaeus, 1758 | parti-colored bat | inhabits Hokkaido and Aomori | ||
| Vespertilio sinensis Peters, 1880 | Asian parti-colored bat | inhabits the area from Hokkaido to Kyushu. | ||
| Myotis bombinus Thomas, 1906 | Far Eastern Myotis | formerly known as M. nattereri | inhabits the area from Honshu to Kyushu | |
| Myotis gracilis Ognev, 1927 | Ussuri whiskered bat | inhabits Hokkaido | ||
| Myotis frater Allen, 1923 | fraternal Myotis | inhabits Hokkaido and northern part of Honshu | ||
| Myotis ikonnikovi Ognev 1912 | Ikonnikov's Myotis | inhabits the area from Hokkaido to Kyushu | ||
| Myotis macrodactylus Temminck, 1840 | Japanese large-footed bat | inhabits the area from Hokkaido to the Amami Islands | ||
| Myotis petax Hollister, 1912 | eastern water bat | inhabits Hokkaido | ||
| Myotis pruinosus Yoshiyuki, 1971 | frosted Myotis | endemic to Japan | inhabits the area from Honshu to Kyushu | |
| Myotis rufoniger Tomes, 1858 | red and black Myotis | formerly known as M. formosus | inhabits Tsushima Island | |
| Myotis yanbarensis Maeda & Matsumura, 1998 | Yanbaru Myotis | endemic to Japan | inhabits the Amami Islands and Okinawa-jima | |
| Murina hilgendorfi Peters, 1880 | Hilgendorf's tube-nosed bat | inhabits the area from Hokkaido to Kyushu | ||
| Murina ryukyuana Maeda & Matsumura, 1998 | Ryukyu tube-nosed bat | endemic to Japan | inhabits the Amami Islands and Okinawa-jima | |
| Murina tenebrosa Yoshiyuki, 1970 | gloomy tube-nosed bat | endemic to Japan | inhabits Tsuhima Island | |
| Murina ussuriensis Ognev, 1913 | Ussurian tube-nosed bat | inhabits the area from Hokkaido to Kyushu | ||
| Miniopteridae | Miniopterus fuliginosus Hodgson, 1835 | eastern bent-winged bat | inhabits the area from Honshu to Kyushu | |
| Miniopterus fuscus Bonhote, 1902 | East-asian little bent-winged bat | endemic to Japan | inhabits the area from the Amami Islands to the Yayeyama Islands | |
| Molossidae | Tadarida insignis Blyth, 1861 | Oriental free-tailed bat | inhabits the area from Hokkaido to Kyushu | |
| Tadarida latouchei Thomas, 1920 | Oriental little free-tailed bat | was recorded from Kushinoerabu-jima and Amami-Oshima | ||
＊（EX）means extinct by the
Japanese Red List(Japanese RDB Categories) by MEJ(2014)
http://www.biodic.go.jp/rdb/rdb_f.html<br>
Reference
The Wild Mammals of Japan Second
edition<br>