Malesia is a biogeographical region straddling the boundary of the Indomalaya and Australasia ecozones. Malesia was first identified as a floristic province that included the Malay Peninsula, Indonesia, the Philippines and New Guinea, based on a shared tropical flora derived mostly from Asia but also with numerous elements of the Antarctic flora, including many species in the southern conifer families Podocarpaceae and Araucariaceae. The floristic province overlaps four distinct mammalian faunal regions.

The western part of Malesia, which includes the Malay Peninsula and the islands of Sumatra, Java, Bali, and Borneo, shares the large mammal fauna of Asia, and is known as Sundaland. These islands are on Asia's relatively shallow continental shelf, and were linked to Asia during the ice ages, when sea levels were lower. The eastern edge of Sundaland is the Wallace line, named for Alfred Russel Wallace, the nineteenth-century British naturalist who noted the difference in fauna between islands on either side of the line.

The eastern end of Malesia, which includes New Guinea and the Aru Islands of eastern Indonesia, is linked to Australia by a shallow continental shelf, and shares many marsupial mammal and bird taxa with Australia. New Guinea also has many additional elements of the Antarctic flora, including southern beech (Nothofagus) and gums (Eucalyptus).

The islands between Sundaland and New Guinea, called Wallacea, were never linked to the neighboring continents, and have a flora and fauna that includes Indomalayan and Australasian elements. The Philippines were also never connected to Asia, and have a largely Asian-derived flora, with some Australasian elements, and a distinct mammalian fauna.