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:

Other rare 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.