As compared with its luxuriant flora, Japan suffers a dearth of animal life. Yet Japanese fauna includes at least 140 species of mammals, 450 species of birds, and a wide variety of reptiles, batrachians, and fish. The only primate mammal is the red-faced monkey, the Japanese macaque, found throughout Honshu. The carnivores include the red bear, black bear, and brown bear. Foxes are found throughout Japan, as are badgers. Other fur-bearing animals include the marten, Japanese mink, otter, weasel, and several varieties of seal. Hares and rabbits are numerous, as are rodents, which include squirrels, flying squirrels, rats, and mice, although the common house mouse is not found. Many varieties of bat exist; insectivores include the Japanese mole and shrewmouse. Of the two species of deer, the more common is the small Japanese deer, which has a spotted white coat in summer and a brown coat in winter.

The sparrow, house swallow, and thrush are the most common Japanese birds. Water birds constitute almost 25% of the known species and include the crane, heron, swan, duck, cormorant, stork, and albatross. Songbirds are numerous, the bullfinch and two varieties of nightingale being the best known. Among other common birds are the robin, cuckoo, woodpecker, pheasant, and pigeon.

The coastal waters of Japan teem with fish, which are caught in enormous quantities for use as fresh food or for canning and also for fertilizer. Various seaweeds are also eaten.