Indonesia is second (after Australia) in terms of total endemic species, with 36% of its 1,531 species of bird and 39% of its 515 species of mammal being endemic. Indonesia's 80,000 kilometers (50,000 mi) of coastline are surrounded by tropical seas that contribute to the country's high level of biodiversity.

Indonesia has a range of sea and coastal ecosystems, including beaches, sand dunes, estuaries, mangroves, coral reefs, sea grass beds, coastal mudflats, tidal flats, algal beds, and small island ecosystems.It is one of Coral Triangle countries with the world's greatest diversity of coral reef fish with more than 1,650 species in eastern Indonesia only.