Biological diversity in Japan


caption Map of Japan. (Source: CI/ CABS)

Encompassing more than 3,000 islands of the Japanese Archipelago, this hotspot includes the land area of the nation of Japan (roughly 370,000 km2). In addition to the four main islands (Hokkaido, Honshu, Shikoku and Kyushu) Japan includes a number of smaller island groups, including the Ogasawara-shoto (the Bonin Islands and Iwo or Volcano Islands), Daito-shoto, Nansei-shoto (Ryukyu and Satsun Islands) and the Izu-shoto. Japan is located at the intersection of three of the Earth's tectonic plates, and the slippage of these plates generates forces that result in numerous volcanoes, hot springs, mountains and earthquakes.

Japan stretches from around 22°N to about 46°N latitude, from the humid subtropics in the south to a temperate zone in the north. This latitudinal range, and the country's mountainous terrain (about 73 percent of Japan is mountainous, the highest point being the 3,776-meter Mt. Fujiyama) contribute to Japan's widely varying climate. While the central mountain area of Honshu is one of the snowiest regions on Earth, the Pacific side of Japan is remarkably dry. Yaku-shima, just south of the southern tip of Kyushu, is one of the wettest places on Earth, with annual rainfall of over 5,000 millimeters in some places.

caption The Japanese serow (Capricornis crispus) is just one of 46 mammals endemic to Japan. Increased habitat fragmentation is putting continued pressure on many of the islands' species. (Source: © Jean-Paul Ferrero/ Auscape)

Japan's vegetation ranges from boreal mixed forests of Abies (fir), Picea (spruce) and Pinus (pines) on Hokkaido (and at high elevations in Honshu and Shikoku) to subtropical broadleaf evergreen forests and mangrove swamps in the south. High elevations on Honshu and Shikoku support alpine vegetation, while subalpine vegetation and natural beech forests are distributed throughout the region. The subtropical island chains in the south of Japan support a flora and fauna different from that of the main islands and hold many endemic species.

Unique and Threatened Biodiversity


Japan is home to roughly 5,600 species of vascular plants, about a third of which (1,950 species) are believed to be endemic. On Ogasawara-shoto, there are about 500 native plant species, of which 43 percent are endemic. Japan also has three endemic plant families (Sciadopityaceae, Glaucidiaceae, and Pteridophyllaceae), and about 20 endemic genera, seven of which are represented only by single species.

About 90 of Japan’s native plant genera are considered part of the Arcto-Tertiary Geoflora; plant genera in this group (such as Wisteria and Buckleya) represent ancient lineages that were distributed around the world in the Tertiary Period. The once widespread forests that are home to these genera are now very fragmented, with members of this group having one or more species in two or three disparate parts of the world: southeastern North America, Japan and China. The origins of this odd biogeographic pattern have been a source of speculation since it was discovered nearly 200 years ago.

Prior to the opening of the Sea of Japan some 15 million years ago, the islands that now make up Japan were part of the Asian mainland. Perhaps not surprisingly then, the plant genera that are considered characteristic of the Japanese flora are rather poorly represented on nearby Taiwan, with Japan’s flora having come mostly from east-central China, Korea, and the islands and mainland to the north, whereas Taiwan’s came from the Philippines and southeastern China.

Among Japan’s notable plants are a number of rare, endemic species that are well-known favorites in gardens, both in Japan and around the world in temperate climates. These include Shirane-aoi (Glaucidium palmatum), which has large blue-purple, sometimes white, flowers, and Togakushisgouma (Ranzania japonica), found only in the high mountains from central to northern Honshu. Urahagusa (Hakonechloa macra), a rare local grass that grows in wet, rocky cliffs in the Tokai region of Japan, is a favorite pot and garden plant.



caption Confined to a single population, the Okinawa woodpecker (Sapheopipo noguchii, CR) continues to decline due to a reduction in mature forests. (Source: © C.T. Hanashiro, BirdLife International)

Nearly 370 bird species are known to occur regularly in Japan, although only 13 are endemic. The Okinawa woodpecker (Sapheopipo noguchii, CR) is the only representative of an endemic genus as is the Bonin white-eye (Apalopteron familiare, VU). Found in the Yanbaru Forest in the northern quarter of Okinawa Island, the Okinawa woodpecker was close to extinction in the 1930s, but has recovered to a population of about 146 to 584 birds. Another of the hotspot’s well-known endemic birds is the Okinawa rail (Gallirallus okinawae, EN), which is also confined to Yanbaru. It is thought that only about 900 pairs of this bird survive in the wild. It is still threatened due to logging and alien invasive species. Three Endemic Bird Areas, as defined by BirdLife International, are found within Japan.

Japan also supports some important waterbird populations, including populations of the red-crowned crane (Grus japonensis, EN), resident on Hokkaido. About 85 percent of the world’s hooded cranes (G. monacha, VU) and 40 percent of white-naped cranes (G. vipio, VU) winter at Izumi on Kyushu.

Tragically, Japan has already suffered a crisis of bird extinctions, with a number of species from its southern islands having been lost over the last two centuries. These include the Ryukyu pigeon (Columba jouyi) and Bonin wood-pigeon (C. versicolor), the Bonin thrush (Zoothera terrestris), and the Bonin grosbeak (Chaunoproctus ferreorostris), a monotypic genus. All four of these extinctions were driven primarily by the introduction of exotic species, in particular of rats and cats.


Japan is home to only around 90 species of mammals, but about half of these are endemic to the hotspot. Sado Island, an island less than 1,000 km2 off western Honshu, has two endemic mammals, the Sado shrew (Sorex sadonis, CR) and the Sado mole (Mogera tokudae, EN). There are also six endemic genera of mammals, including three that are monotypic: the Amami rabbit (Pentalagus furnessi, VU), found in the Amami-shoto in the Nansei-shoto, the Japanese dormouse (Glirulus japonicus, EN), found on Honshu and Shikoku, and the Ryukyu long-tailed giant rat (Kiplothrix legatus, EN), restricted to the Ryukyu Islands and the Yanbaru Forest on Okinawa. The Amami rabbit suffered a dramatic decline in the early twentieth century, subsequent to which it was declared a national monument and given complete legal protection, although sadly this protection did not extend to protection of its habitat. Habitat fragmentation and introduced mongooses threaten the rabbit’s survival, and only about 2,500 individuals remain.

One of the best-known mammals in Japan is the Japanese macaque (Macaca fuscata), the most northerly-living monkey in the world, found on Honshu, Shikoku, Kyushu and a few other small islands. These are the famous “snow monkeys” that can be seen playing in the winter snow and warming up in volcanic springs. Another endemic macaque species, the Yaku-shima macaque (M. yakui) is found only on the island of Yaku-shima. The Iriomote cat (Prionailurus iriomotensis), restricted to Iriomote-jima, was first described in 1967, although it may be a subspecies of the leopard cat (P. bengalensis). There are no more than perhaps 100 individuals left on Iriomote-jima.


Japan has over 65 reptile species, almost 30 of which are endemic. The reptile fauna includes a number of important threatened species: the Okinawa black-breasted leaf-turtle (Geoemyda japonica, EN), the Kikuzato’s brook snake (Opisthotropis kikuzatoi, CR), found only on the Kume-jima in the Okinawashoto in the Ryukyus, the Amami takachiho snake (Achalinus werneri, VU), confined to Amami, and the Tokashiki ground gecko (Goniurosaurus kuroiwae, VU), from the Ryukyus.


Endemism is particularly high among amphibians, with 44 of 50 species found only in Japan. The amphibian genus Hynobius is very well represented, with about 15 of the 25 known species worldwide being endemic to the hotspot, one of which, the Oki salamander (H. okiensis, CR), is confined entirely to Dogo, of the Okino-shima in Shimane Prefecture. The Japanese giant salamander (Andrias japonicus), found in western Honshu, Shikoku and Kyushu, can grow to more than one meter in length and is one of the world’s largest amphibians. Once threatened by human consumption, the salamander is now considered a natural monument and protected by law.

Freshwater Fishes

The hotspot has a relatively small freshwater fish fauna, with almost 215 native species, more than 50 of which are endemic. While most inland waters are dominated by fishes entering from the sea, there is also a significant representation of strictly freshwater groups, including minnows (Cyprinidae) and loaches (Cobitidae and Balitoridae) that have diversified within the hotspot and account for nearly half of the endemic species and three of four endemic genera. The occurrence of five lampreys and four sturgeons from ancient lineages mean that Japan also holds a disproportionately large amount of the evolutionary history of fishes.


Some invertebrate groups are very well documented in Japan. For example, nearly 240 butterfly species are thought to be native to Japan (although this includes naturalized species), and nearly 25 species of tiger beetles are recorded from the hotspot (about a quarter of which are endemic).

Human Impacts

caption The Okinawa rail (Gallirallus okinawae, EN) is represented by a single population in the Yambaro Forest on northern Okinawa. Development, especially golf course construction, and introduced predators are two threats facing this species. (Source: © C.T. Hanashiro, BirdLife International)

Because so much of the Japanese population (estimated at around 127.5 million ppl) lives in such a small percentage of the country (70 percent on three percent of the land), much of the remaining areas of Japan are quite undeveloped. Notwithstanding, only about 20 percent of the country's original vegetation is thought to remain intact.

Following World War II, the Forestry Agency of Japan promoted clear-cutting of the high-elevation conifer forests and replaced them with Japanese timber species such as sugi (Cryptomeria japonica) and Kara-matsu (Larix leptolepis). Today, plantations are widespread on Japan. However, unlike many other hotspots, Japan's remaining forests are not facing elevated threat due to logging, owing to the high cost of Japanese timber compared to cheap imports from other countries.

On the other hand, Japan's affluence, its recently reduced workweek and the resultant increased interest in leisure have put a different type of strain on the natural environment. Forests are being cleared for ski resorts and golf courses, and more roads are being built to accommodate the steady increase in automobiles and the growing desire to use private rather than public transportation. In addition, improvements in public transportation, such as the bullet train, have made it even easier to travel to once remote and little developed areas of the country.

Coastal regions and wetlands are also being lost to development, principally agricultural expansion, river channelization and road building. On Hokkaido, the wetlands favored by nesting red-crowned cranes continue to be lost to development, mainly agricultural expansion, river channelization, and road building. For instance, one-third of almost 300 km2 of marshland in Kushiro has been converted to agricultural, industrial or residential use since the 1970s.

As on the main islands, the smaller islands of the Ryukyus and Ogasawaras have lost habitat to timber plantations and urban development. Nearly all the original subtropical forest on the Ogasawaras has been cleared, and in the Ryukyus, only small areas remain on Amami and Okinawa, mainly in protected areas.

Finally, invasive alien plants and animals pose a threat to the native fauna and flora of Japan. Some of these species, including the Indian grey mongoose (Herpestes edwardsi), Javan mongoose (H. javanicus) and Siberian weasel (Mustela sibirica) were introduced for the purposes of snake control but have instead caused significant declines of many native birds and small mammals. Introduced goats are a problem on several islands, and large mouth bass (Micropterus salmoides) pose a serious threat to native fishes throughout the hotspot.

Conservation Action and Protected Areas

caption Known to bathe in Japan's volcanic springs, the Japanese macaque or snow monkey (Macaca fuscata) is the most northerly-living non-human primate in the world. (Source: © Jean-Paul Ferrero/ Auscape)

Japan has 28 national parks, and many quasi-national parks, prefectural natural parks and prefectural wildlife protection areas. About six percent of the hotspot (21,918 km2), falls within protected areas classified in IUCN categories I to IV. However, when other forms of legally protected areas are included, this number rises to about 17 percent of the hotspot. Japan also has two Natural World Heritage Sites, Shirakami-sanchi in northern Honshu, and Yaku-shima in the Satsunan-shoto, which contains ancient Japanese cedar trees.

The main gap in the protected area system is in the Ryukyus, where most forested areas are not properly protected. For example, Yanbaru, which is home to important populations of six of the 32 Critically Endangered and Endangered species in Japan, including the entire global populations of Okinawa rail and Okinawa woodpecker, is unprotected. While a quarter of the forest is in the U.S. Marine Corps Training Area, the rest is threatened by clear-cutting and removal of forest undergrowth.

Concern for the environment is widespread in Japan. The Cosmos Prize, one of the world's top environmental awards, was established by the Expo '90 Committee to honor those who have promoted the harmonious coexistence of nature and humankind. The prize has focused public attention on the need for conservation. Japan has also become a significant player in international biodiversity conservation. For example, the Japanese Government is one of five partners in the Critical Ecosystem Partnership Fund (along with the World Bank, the Global Environment Facility, the MacArthur Foundation and Conservation International), which is providing $125 million over five years for conservation in the hotspots.

Further Reading

  • Abe, H. 1994. A Pictorial Guide to the Mammals of Japan. Japan: Tokai University Press.
  • Anonymous. 2004. Climate of Japan. March 17, 2004.
  • BirdLife International. 2003. Saving Asia's Threatened Birds: A Guide for Government and Civil Society. Cambridge, U. K. Birdlife International.
  • Expo '90 Foundation. International Cosmos Prize. February 2, 2004.
  • Fitzhugh, W.W. & Dubreil, C.O. (Eds.). 2000. Ainu: Spirit of a Northern People. Arctic Studies Center, National Museum of Natural History. Seattle: Smithsonian Institution in association with University of Washington Press. ISBN: 0967342902.
  • Hara, H. & Kanai, H. 1958. Distribution Maps of Flowering Plants in Japan, Part 1. Tokyo: Inoue Book Company.
  • Hara, H. 1959. An outline of the phytogeography of Japan. In H. Hara. & H. Kanai. (Eds.), Distribution Maps of Flowering Plants in Japan, Part 2. pp. 1-96. Tokyo: Inoue Book Company.
  • Ito, Y., Miyagi, K. & Ota, H. 2000. Imminent extinction crisis among the endemic species of the forests of Yanbaru, Okinawa, Japan. Oryx 34(4):305-316
  • Iwatsuki, K., Yamazaki, T., Boufford, D.E. & Ohba, H. (Eds.). 1993. Flora of Japan, Vol. IIIa: Angiospermae, Dicotyledoneae, Sympetalae (a). Tokyo: Kodansha, Ltd.
  • Iwatsuki, K., Yamazaki, T., Boufford, D.E. & Ohba, H. (Eds.). 1995a. Flora of Japan, Vol. IIIb: Angiospermae, Dicotyledoneae, Sympetalae (b). Tokyo: Kodansha, Ltd.
  • Iwatsuki, K., Yamazaki, T., Boufford, D.E. & Ohba, H. (Eds.). 1995b. Flora of Japan, Vol. I: Pteridophyta and Gymnospermae. Tokyo: Kodansha, Ltd.
  • Iwatsuki, K., Boufford, D.E. & Ohba, H. (Eds.). 2001. Flora of Japan, Vol. IIb: Angiospermae; Dicotyledonieae; Archichlamideae(b). Tokyo: Kodansha, Ltd.
  • Kitayama, K. 1991. Threatened endemic species of the Bonin (Ogasawara) Islands. Pac. Sci. Assoc. Inform. Bull. 43(3/4):9-10.
  • Kurosawa, R. & Askins, R. A. 2003. Effects of habitat fragmentation on birds in deciduous forests in Japan. Conservation Biology 17: 695-707.
  • Li, H. L. 1971. Floristic Relationships between Eastern Asia and North America. Reprinted with a foreword from the Transactions of the American Philosophical Society, New Series, Vol. 42, part 2, 1952.
  • Maeda N. & Matsui M. 1999. Frogs and Toads of Japan plus Salamander. Tokyo: Bun-Ichi Shuppan Co. Ltd.
  • Masuda, H., Amaoka, K., Araga, C., Uyeno, T. & Yoshino, T. 1984. The Fishes of the Japanese Archipelago. Fish: Tokai University Press. ISBN: B000W00NAA.
  • Ministry of the Environment, Government of Japan. 2004. Policies & Programs. National Strategy Of Japan On Biological Diversity. Section 3 Species and Genetic Diversity. January 29, 2004.
  • Ministry of the Environment, Government of Japan. 2004. State of Japan's Environment at a Glance: Natural Vegetation. January 29, 2004.
  • Ministry of the Environment, Government of Japan. 2004. State of Japan's Environment at a Glance: National Parks and Sanctuaries. January 29, 2004.
  • Mueller-Dombois, D. & Fosberg, F.R. 1998. Vegetation of the Tropical Pacific Islands. New York: Springer-Verlag. ISBN: 038798285X.
  • Numata, M. 1974. The Flora and Vegetation of Japan. Tokyo: Kodansha, Ltd. ISBN: 0444998802.
  • Ohwi, J. 1965. Flora of Japan (In English). Washington, D.C.: Smithsonian Institution. ISBN: 0874747082.
  • Pietsch, T. W., Bogatov, V. V., Amaoka, K., Zhuravlev, Y. N., Barkalov, V. Y., Gage, S., Takahashi, H., Lelej, A. S., Storozhenko, S. Y., Minakawa, N., Bennett, D. J., Anderson, T. R., Ohara, M., Prozorova, L. A., Kuwahara, Y., Kholin, S. K., Yabe, M., Stevenson, D. E. & MacDonald, E. L. 2003. Biodiversity and biogeography of the islands of the Kuril Archipelago. Journal of Biogeography 30: 1297-1310.
  • Sibatini, A. 1990. Decline and conservation of butterflies in Japan. Journal of Research on the Lepidoptera 29: 305-315
  • Watanabe, S. 2004. Japanese View of Nature. Kankyou Kaigi, Spring 2004. Tokyo. Senden Kaigi, Ltd.
  • WBSJ. 1982. A Field Guide to the Birds of Japan. Tokyo: Wild Bird Society of Japan. ISBN: 0870117467.
  • Wen, J. 1999. Evolution of eastern Asian and eastern North American disjunct pattern in flowering plants. Ann. Rev. Ecol. Syst. 30: 421-455.
  • Wikramanayake, E.D., Dinerstein, E., Loucks, C., Olson, D., Morrison, J., Lamoreux, J., McKnight, M. & Hedao, P. (Eds.). 2002. Terrestrial Ecoregions of the Indo-Pacific: A Conservation Assessment. Washington, D.C.: Island Press. ISBN: 1559639237.

Disclaimer: This article is taken wholly from, or contains information that was originally published by, the Conservation International. Topic editors and authors for the Encyclopedia of Earth may have edited its content or added new information. The use of information from the Conservation International should not be construed as support for or endorsement by that organization for any new information added by EoE personnel, or for any editing of the original content.



International, C. (2008). Biological diversity in Japan. Retrieved from


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