Daftar spesies mamalia di Jepang
Ordo: Chiroptera (kelelawar)

Ryukyu flying fox, little Japanese horseshoe bat, northern bat, Endo's pipistrelle, parti-coloured bat, Hodgson's bat, big-footed myotis, Hilgendorf's tube-nosed bat, Ussuri tube-nosed bat, eastern bent-wing bat
Ciri khas kelelawar yang paling menonjol adalah bahwa kaki depan mereka berkembang menjadi sayap, menjadikan mereka satu-satunya mamalia yang mampu terbang. Spesies kelelawar mencakup sekitar 20% dari semua mamalia.
Family: Pteropodidae (flying foxes, Old World fruit bats)
Subfamily: Pteropodinae
Genus: Pteropus
Ryukyu flying fox, Pteropus dasymallus VU IUCN (Ryūkyū Islands)
Daito flying fox, P. d. daitoensis (MOE: CR) (Daitō Islands; Natural Monument)
Erabu flying fox, P. d. dasymallus (MOE: CR) (Ōsumi Islands and Tokara Islands)
Orii's flying fox, P. d. inopinatus
Yaeyama flying fox, P. d. yayeyamae
Okinawa flying fox, Pteropus loochoensis DD IUCN (MOE: EX) (not found since a C19 record)
Bonin flying fox, Pteropus pselaphon EN IUCN (MOE: EN) (endemic to Bonin Islands and Volcano Islands)
Family: Hipposideridae
Genus: Hipposideros
Lesser great leaf-nosed bat, Hipposideros turpis EN IUCN (endemic to Yaeyama Islands)
Family: Rhinolophidae
Genus: Rhinolophus
Greater horseshoe bat, Rhinolophus ferrumequinum LC IUCN (widely distributed)
Imaizumi's horseshoe bat Rhinolophus imaizumii (endemic)
Little Japanese horseshoe bat, Rhinolophus cornutus (NR) (endemic; widely distributed)
R. c. cornutus
Orii's least horseshoe bat, R. c. orii (MOE: EN) (Amami Islands)
Okinawa little horseshoe bat [ ja] , Rhinolophus pumilus (NR) (endemic to Okinawa)
Okinawa little horseshoe bat [ja], R. p. pumilus (MOE: EN) (Okinawa)
Miyako little horseshoe bat [ja], R. p. miyakonis (MOE: EX) (Miyako Island)
Yaeyama little horseshoe bat, Rhinolophus perditus EN IUCN (MOE: VU) (endemic to the Yaeyama Islands)
Family: Molossidae
Genus: Tadarida
East Asian free-tailed bat, Tadarida insignis DD IUCN (MOE: VU) (not found in Okinawa)
La Touche's free-tailed bat, Tadarida latouchei EN IUCN (MOE: DD) (Amami Islands, Kuchinoerabu-jima)
Family: Miniopteridae
Genus: Miniopterus
Eastern bent-wing bat, Miniopterus fuliginosus (NR) (Honshū, Shikoku, Kyūshū, and adjacent smaller islands)
Southeast Asian long-fingered bat, Miniopterus fuscus EN IUCN (MOE: EN) (endemic to Ryūkyū Islands)
Family: Vespertilionidae
Subfamily: Vespertilioninae
Genus: Eptesicus
Japanese short-tailed bat, Eptesicus japonensis VU IUCN (MOE: VU) (endemic; central Honshū)
Northern bat, Eptesicus nilssoni LC IUCN (Hokkaidō, Kunashiri, Etorofu)
Genus: Nyctalus
Birdlike noctule, Nyctalus aviator NT IUCN (MOE: VU) (widely distributed)
Japanese noctule, Nyctalus furvus EN IUCN (MOE: EN) (endemic; central and northern Honshū)
Genus: Pipistrellus
Japanese pipistrelle, Pipistrellus abramus LC IUCN (widely distributed)
Endo's pipistrelle, Pipistrellus endoi NT IUCN (MOE: VU) (endemic; Honshū and Shikoku)
Sturdee's pipistrelle, Pipistrellus sturdeei EX IUCN (MOE: EX) (endemic; not found since the type specimen was collected on Hahajima in 1915)
Genus: Barbastella
Asian barbastelle, Barbastella leucomelas LC IUCN
Eastern barbastelle, B. l. darielingensis (Hokkaidō, Kunashiri, Honshū and Shikoku)
Genus: Plecotus
Japanese long-eared bat, Plecotus sacrimontis LC IUCN (endemic; not found in Okinawa)
Genus: Hypsugo
Alashanian pipistrelle, Hypsugo alaschanicus LC IUCN (MOE: DD) (found in Hokkaidō and Aomori, and on Tsushima Island)
Savi's pipistrelle, Hypsugo savii LC IUCN
Genus: Vespertilio
Particoloured bat, Vespertilio murinus LC IUCN (MOE: DD) (found in Hokkaidō, Aomori, and Ishikawa)
Asian particoloured bat, Vespertilio sinensis LC IUCN (widely distributed; not found in Okinawa)
Subfamily: Myotinae
Genus: Myotis
Reddish-black myotis, Myotis rufoniger LC IUCN (MOE: CR) (as Hodgson's bat, Myotis formosus) (found on Tsushima)
Fraternal myotis, Myotis frater DD IUCN (north from Gifu)
Ussuri whiskered bat, Myotis gracilis LC IUCN (as Siberian bat Myotis sibiricus) (MOE: VU) (Hokkaidō, Kunashiri, Etorofu)
Ikonnikov's bat, Myotis ikonnikovi LC IUCN (Hokkaidō, Kunashiri, Honshū)
M. i. hosonoi
M. i. ikonnikovi
Big-footed myotis, Myotis macrodactylus LC IUCN (widely distributed)
Far Eastern myotis, Myotis bombinus NT IUCN (MOE: VU) (as Myotis nattereri bombinus) (widely distributed; not found in Okinawa)
Eastern water bat, Myotis petax LC IUCN (Hokkaidō, Kunashiri, Etorofu)
Frosted myotis, Myotis pruinosus EN IUCN (MOE: VU) (endemic; Honshū, Shikoku, Kyūshū)
Yanbaru whiskered bat, Myotis yanbarensis CR IUCN (MOE: CR) (endemic to Ryūkyū Islands)
Subfamily: Murininae
Genus: Murina
Hilgendorf's tube-nosed bat, Murina hilgendorfi LC IUCN (widely distributed; not found in Okinawa)
Ryukyu tube-nosed bat, Murina ryukyuana EN IUCN (MOE: EN) (endemic to Ryūkyū Islands)
Gloomy tube-nosed bat, Murina tenebrosa CR IUCN (MOE: DD) (endemic; not found since the type specimen was collected on Tsushima Island in 1962)
Ussuri tube-nosed bat, Murina ussuriensis LC IUCN (widely distributed; not found in Okinawa)