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 biogeographical realms, large-scale divisions of the Earth's surface based on the historic and evolutionary distribution patterns of plants and animals. Realms are subdivided into bioregions (and marine realms into provinces), which are in turn made up of multiple ecoregions. The Indomalayan realm extends across the western half of the archipelago, and the eastern half is in the Australasian realm. 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 the 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 elephants, 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.

• Borneo lowland rain forests (Borneo, Natuna Islands)
• Borneo montane rain forests (Borneo)
• Borneo peat swamp forests (Borneo)
• Eastern Java–Bali montane rain forests (Bali, Java)
• Eastern Java–Bali rain forests (Bali, Java)
• Mentawai Islands rain forests (Mentawai Islands)
• Peninsular Malaysian rain forests (Anambas Islands, Lingga Islands, Riau Archipelago)
• Southwest Borneo freshwater swamp forests (Borneo)
• Sumatran freshwater swamp forests (Sumatra)
• Sumatran lowland rain forests (Sumatra, Nias, Bangka)
• Sumatran montane rain forests (Sumatra)
• Sumatran peat swamp forests (Sumatra)
• Sundaland heath forests (Borneo, Bangka, Belitung)
• Western Java montane rain forests (Java)
• Western Java rain forests (Java)

• Sumatran tropical pine forests (Sumatra)

• Sunda Shelf mangroves (Borneo, Sumatra, Riau Islands)

• Banda Sea Islands moist deciduous forests (Banda Islands, Kai Islands, Tanimbar Islands, Babar Islands, Leti Islands, eastern Barat Daya Islands)
• Buru rain forests (Buru)
• Halmahera rain forests (Halmahera, Morotai, Obi Islands, Bacan Island)
• Seram rain forests (Seram, Ambon Island, Saparua, Gorong Islands)
• Sulawesi lowland rain forests (Sulawesi, Banggai Islands, Sula Islands, Sangihe Islands, Talaud Islands)
• Sulawesi montane rain forests (Sulawesi)

• Lesser Sundas deciduous forests (Lombok, Sumbawa, Komodo, Flores, Alor)
• Sumba deciduous forests (Sumba)
• Timor and Wetar deciduous forests (Timor, Wetar)

• Biak–Numfoor rain forests
• Central Range montane rain forests
• Northern New Guinea lowland rain and freshwater swamp forests
• Northern New Guinea montane rain forests
• Southern New Guinea freshwater swamp forests
• Southern New Guinea lowland rain forests
• Vogelkop montane rain forests
• Vogelkop–Aru lowland rain forests
• Yapen rain forests

• Trans-Fly savanna and grasslands

• Central Range sub-alpine grasslands

• New Guinea mangroves

• Borneo Highlands

• Aceh
• Central & Eastern Java
• Eastern Borneo
• Indian Ocean Slope of Sumatra & Java
• Kapuas
• Malay Peninsula Eastern Slope
• Northeastern Borneo
• Northern Central Sumatra - Western Malaysia
• Northern Philippine Islands
• Northwestern Borneo
• Southeastern Borneo
• Southern Central Sumatra
• Southern Sumatra - Western Java

• Lake Poso
• Matano - Southern Malili Lakes

• Lesser Sunda Islands
• Maluku; (Indonesia)
• Sulawesi

• New Guinea Central Mountains
• New Guinea North Coast

• Southwest New Guinea - Trans-Fly Lowland
• Vogelkop - Bomberai

• Western Sumatra

• Sunda Shelf/Java Sea
• Malacca Strait

• Southern Java

• Palawan/North Borneo
• Sulawesi Sea/Makassar Strait
• Halmahera
• Papua
• Banda Sea
• Lesser Sunda
• Northeast Sulawesi

• Arafura Sea

• Wikramanayake, Eric; Eric Dinerstein; Colby J. Loucks; et al. (2002). Terrestrial Ecoregions of the Indo-Pacific: a Conservation Assessment. Island Press; Washington, DC.
• Freshwater Ecoregions of the World
• Abell, R., Michele L. Thieme, Carmen Revenga, Mark Bryer et al. "Freshwater Ecoregions of the World: A New Map of Biogeographic Units for Freshwater Biodiversity Conservation". Bioscience Vol. 58 No. 5, May 2008, pp. 403-414.
• Spalding, Mark D., Helen E. Fox, Gerald R. Allen, Nick Davidson et al. "Marine Ecoregions of the World: A Bioregionalization of Coastal and Shelf Areas". Bioscience Vol. 57 No. 7, July/August 2007, pp. 573–583.