Despite the high population density, forest cover is very high (69%), in European framework comparable only to Scandinavian countries. Forest types: boreal coniferous forest at Hokkaido, temperate mixed and broadleaved forests at Honshu, evergreen subtropical forests at Kyushu and Shikoku and tropical vegetation at Ryukyu. Wel-developed zonation of vegetation, alpine meadows above tree limit, top of Fuji-san almost all the year covered by snow. Soils vary from laterites on the south to podzols on the north. Abundant volcanic soils called andosols, the name of which is derived from Japanese words an-do that means "black soil."
Thanks to wide range of latitude, altitude and isolation from Asia mainland, Japan is characteristic by exceptional biodiversity, much higher then in the case of European countries with comparable area. There are, for example, 5,565 vascular plants species, 90 mammal species and 63 species of reptiles. Relatively high proportion of endemic species. Ryukyu and Ogawara islands are even called Galapagos of the East (Source: Ministry of Environment of Japan).
Fauna is similar to adjacent parts of Asia, thanks to isolation from it several endemic species:
- Iriomote cat, Felis iriomotensis - the rarest cat in the world living only at Iriomote (Southermost island of Ryukyu archipelago), discovered as late as1964
- Giant salamander, Megalobatrachus maximus - the largest aphibian in the world (up to 1,5 m)
- Japanese badger, Meles meles anakuma
- Japanese snow monkey, Macaca fuscata - northernmost distributed monkey in the world, able to cope with as low temperatures as minus 15o C
- Japanese otter or Japanese river otter, Lutra nippon - many times considered only as subspecies of Eurasian otter (Lutra lutra nippon), endangered species surviving at Shikoku
- Japanese serow, Capricornis crispus crispus (syn. Nemorhaedus crispus) - endemic species of short-horned goat antelope living in the dense mountain forests in altitudes above 1000 metres together with its relatives - gorals. Japanese subspecies is significantly smaller than continental one. This species was overhunted in the past, but now it is quite common and can damage to the forest stands.
- Japanese marten of Tsushima Island, Martes melampus tsuensis - the subspecies classified as indeterminate by the IUCN Red List. (Nominal subpecies of Japanese marten is also present in Japan, however, its distrubution is not restricted to Japan.)
- Bonin fruit bat, Pteropus pselaphon - "Flying fox" from Bonin island, large endemic Fruit bat, endangered species
Other rare species:
- Japanese crane, Grus japoniensis - one of the symbols of Japan surviving on Hokkaido (Kushiro marshland)
- Crested ibis, Nipponia nippon - despite the japanese-sounding name, areal of this species includes not only Japan, but also parts of China, Russia and Korea. Now it represent one of the most endangered bird species.
Other significant species: Hokkaido bear (Ursus arctos yesoensis) living on Hokkaido, Japanese black bear (Ursus thibetanus japonicus) - smaller bear living in Japan excluding Hokkaido
Flora is characterised by large proportion of endemic species (as for vascular plants it is more than 35%, out of which 2 families and 20 genera are endemic)
Present-day high population density threatens many species as well as their habitats.
Nature reserves: network of 27 national parks (5% of the total area of Japan) effectively secures the protection & conservation of almost all significant natural habitats of Japan. There are also so-called "qausi-national parks" in Japan. The only difference between them and "genuine" national parks is that they are officially proclaimed, protected and administered by prefecture authorities.