List of Ecoregions in Indonesia

The following is a list of ecoregions in Indonesia. An ecoregion is defined by the WWF as a "large area of land or water that contains a geographically distinct assemblage of natural communities". There are terrestrial, freshwater, and marine ecoregions. Ecoregions classified into biomes or major habitat types.

Indonesia straddles two of the Earth's terrestrial ecozones, large-scale divisions of the Earth's surface based on the historic and evolutionary distribution patterns of plants and animals. Ecozones are subdivided into bioregions, which are in turn made up of multiple ecoregions. Indomalaya ecozone extends across the western half of the archipelago, and the eastern half is in Australasia. The Wallace Line, which runs between Borneo and Sulawesi, Bali and Lombok, is the dividing line.

The portion of Indonesia west of the Wallace Line is known as Sundaland bioregion, which also includes Malaysia and Brunei. When sea levels fell during the Ice Ages, the shallow Sunda Shelf was exposed, linking the Islands of Sundaland to the Asian continent. Sundaland has many large mammals of Asian origin, including rhinoceros, Asian Elephant, and apes.

East of the Wallace Line lies the Wallacea bioregion, made up of islands that were never linked to a continent, but were instead pushed up by the Australian continent's northward movement. Wallacea is a transitional region between Asia and Australia. It has a flora of mostly Indomalayan origin, with elements from Australasia, with a reptile and bird fauna of mainly Australian origin and no large mammal fauna.

The Aru Islands and the Indonesian portion of New Guinea are connected by the shallow Sahul Shelf to the Australian continent, and were connected by land during the Ice Ages. New Guinea has a flora of chiefly Asian origin with many Australasian elements, and a fauna similar to that of Australia.