exclusively in Japan include the Japanese Macaque (ARKive),
the Japanese Serow (Ultimate
Ungulate), the Iriomote Cat (JTEF),
the Japanese Badger (ARKive),
the Japanese Weasel (ARKive),
the Japanese Giant Flying Squirrel (eol),
the Japanese Dwarf Flying Squirrel (Kumamoto
Eco), the Japanese Noctule (ARKive),
and the Bonin Flying Fox (Fruit
Bat World). Endemic genera include the Amami Rabbit
the Japanese Dormouse (EDGE),
the Ryukyu Long-tailed Giant Rat (Univ.
Ryukyus), the Okinawa Spiny Rat (EDGE),
True’s Shrew Mole (Sendai
Science Museum), and the Japanese Shrew Mole (Planet'
Mammiferes). Three full
sika deer species are considered endemic to Japan by some
classifications including Cervus
in Tsushima, Cervus
from Hokkaido and northern Honshu, and Cervus nippon (flickr)
from southern Japan.
Birds unique to Japan include the Okinawan Woodpecker (ARKive), the Bonin White-eye (ARKive), the Amami Jay (ARKive), the Short-tailed Albatross (ARKive), the Okinawa Rail (ARKive), the Japanese Night Heron (HBW), the Copper Pheasant (ARKive), the Green Pheasant (flickr), the Izu Thrush (OBC), Ijima’s Leaf Warbler (OBC), the Ryukyu Robin (ARKive), the Ryukyu Minivet (flickr), the Japanese Yellow Bunting (avesphoto.com), the Japanese Wagtail (HBW), the Japanese Woodpecker (HBW), and the Amami Woodcock (HBW).
Reptiles found only in Japan include the Yaku Gecko (Japanese Reptiles), the Okinawa Ground Gecko (ARKive), the Green Grass Lizard (Japanese Reptiles), the Ryukyu Short-legged Skink (Japanese Reptiles), Kishinoue’s Giant Skink (Japanese Reptiles), the Hyan Coral Snake (Japanese Reptiles), the Tokarahabu (Japanese Reptiles), the Tsushima Mamushi (Japanese Reptiles), the Himehabu (Japanese Reptiles), the Amami Odd-scaled Snake (ARKive), Pryer’s Keelback (Japanese Reptiles), the Ryukyu Green Snake (Japanese Reptiles), and the Japanese Pond Turtle (flickr).
Amphibians restricted to Japan include the Japanese Giant Salamander (ARKive), the Oki Salamander (ARKive), the Japanese Clawed Salamander (AmphibiaWeb), the Japanese Fire-bellied Newt (Caudata Culture), the Japanese Stream Toad (AmphibiaWeb), Hallowell’s Tree Frog (Japanese Frogs), the Okinawa Rice Frog (flickr), Namie’s Frog (Univ. Ryukyus), the Amami Tip-nosed Frog (AmphibiaWeb), Ishikawa's Frog (ARKive), the Kajika Frog (Japanese Frogs), and the Forest Green Tree Frog (AmphibiaWeb).
Endemic freshwater fish genera include Biwia (FishBase), Hemigrammocypris (eol), and Ischikauia (memobird). Other endemic freshwater fish include the Japanese Spined Loach (ARKive), the Nekogigi (ARKive), the Lake Biwa Catfish (FishBase), the Tokyo Bitterling (flickr), the gobies Gymnogobius isaza (LBM) and Stiphodon imperiorientis (ARKive), and a sculpin Cottus reinii (LBM). Endemic marine fish include the Izu Stingray (Izuzuki Diver), Shiho’s Seahorse (eol), the Orange Pipefish (fishpix), the Japanese Dragonet (eol), the Whitebar Anthias (Izuku Diver), the Izu Islands Triplefin (Izuzuki Diver), Takeuchi's Angelfish (eol), Tanaka's Dottyback (fishpix), a parrotfish Scarus obishime (eol), and a soldierfish Myripristis kochiensis (fishpix).
Butterflies known solely from Japan include the Gifu Swallowtail (ARKive), the Fujisan Green Hairstreak (ze-ph.sakura.ne.jp), and the Jezo Green Hairstreak (Butterflies of Okutama). Other endemic insects include the Genji Firefly (Yoshihito Furukawa), the Japanese Owl Moth (Japanese Moths), a relict dragonfly Epiophlebia superstes (Odonata of Kobe), a cicada Platypleura yayeyamana (Cicadae in Japan), a tiger beetle Cicindela bonina (hanmyou), the Jambar Long-armed Beetle (Univ. Ryukyus), an ant Camponotus bishamon (Japanese Ant ID), and the mayfly family Dipteromimidae (Mostly About Mayflies).
endemic invertebrates include Semisulcospira
freshwater snails (Bishogai),
land snails Hirasea
and Euhadra quaesita
a land crab Geothelphusa tenuimana
Ryukyus), a millipede Riukiaria holstii (flickr),
the sea slugs Noumea
Slug Forum) and Melibe
Slug Forum). Endemic families
include earthworms Biwadrilidae (p. 5 of Opuscula
Zoologica pdf file) (LBERI
amphipods Luciobliviidae (Wiley),
copepods Protolatiremidae (p. 58 of HUSCAP
pdf file), harvestmen Nippononychidae (Opiliones
tardigrade Thermozodiidae (Google
Books), and a hemichordate Atubaridae (J-STAGE
Endemic genera include the Nippon Daisy (Plant Kaleidoscope), the Satake Palm (PACSOA), the Japanese Forest Grass (BBC), the Asunaro (Wikipedia), Ranzania (wildplants.sakura.ne.jp), Dendrocacalia (ogasawara-syokubutusi), Glaucidium (World Natural Heritage), Ancistrocarya (hanamist.sakura.ne.jp), Pteridophyllum (Botanic Garden), Perillula (Masao Takeno), Japonolirion (alpine-plants-jp.com), Miricacalia (Japanese Wild Flowers), Anemonopsis (alpine-plants-jp.com), Boninia (ogasawara-syokubutusi), Comospermum (Asian Flora), Apodicarpum (Masato Ohtani), Chamaele (Botanic Garden), and the recently described Nihon (flickr). The Japanese Umbrella Pine (ARKive) is the sole member of the endemic family Sciadopityaceae.
Japan is its own biodiversity hotspot (CEPF). Japan has exceptional marine endemism and portions of the country are included in the Southern Japan, Taiwan and Southern China coral reef hotspot (Columbia Univ. pdf file). Lake Biwa (LBM) is one ot the world's most ancient lakes and has many unique species.