Malesia is a biogeographical region straddling the Equator and the boundaries of the Indomalayan and Australasian realms. It is a phytogeographical floristic region in the Paleotropical kingdom. It was first recognized as a distinct region in 1857 by Heinrich Zollinger, a Swiss botanist and explorer. The precise boundaries used to define Malesia vary. The broadly defined area used in Flora Malesiana consists of the countries of Malaysia, Singapore, Indonesia, Brunei, the Philippines, Timor-Leste and Papua New Guinea. The original definition by the World Geographical Scheme for Recording Plant Distributions (WGSRPD) covered a similar area, but New Guinea and some offshore islands were split off as Papuasia in its 2001 version.

Malesia was first recognized as a distinct floristic region in 1857 by Heinrich Zollinger, a Swiss botanist and explorer. In 1948 and 1950, Cornelius G. G. J. van Steenis developed the idea of Malesia, and put forward plans for a Flora Malesiana. Van Steenis defined the area of Malesia through the concept of 'demarcation knots': lines across which there are major changes in the genera present in the flora. There were three clear boundaries: between the Malay Peninsula (including part of southern Thailand) and mainland Asia (line 1 in map 2); between the Philippines and Taiwan (line 2 in map 2); and along the Torres Strait between New Guinea and Australia (line 3 in map 2). The eastern boundary was less clear; van Steenis somewhat arbitrarily placed it between the Bismarck and Solomon Islands and the other Pacific islands (line 4 in map 2). Van Steenis initially used Zollinger's name 'Malesia'. He later anglicized it to 'Malaysia', but when the country of Malaysia was formed in 1963, it was necessary to return to the original name.

The first edition of the World Geographical Scheme for Recording Plant Distributions (WGSRPD) used the same definition, but in the second edition of 2001, New Guinea and the Bismarck Archipelago were removed from Malesia and united with the Solomon Islands, previously placed in the WGSRPD's Southwestern Pacific region, and placed into a new region, Papuasia, whose eastern boundary extends to line 5 in map 2.

Using the Flora Malesiana definition, Malesia has a shared tropical flora derived mostly from Asia, but also with numerous elements of the Antarctic flora. Malesia is a hotspot of global biodiversity. In 1995, it was estimated that there were 42,000 species of vascular plants, of which 70% were endemic. By comparison, Europe, which is about three times the area, had 11,000 species of vascular plants, of which about 30% were endemic.

Western Malesia includes the Malay Peninsula and the islands of Sumatra, Java, Bali, and Borneo (area A in map 2). It 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 south-eastern edge of Sundaland (line 6 in map 2) is the Wallace Line, named after Alfred Russel Wallace, the nineteenth-century British naturalist who noted the difference in fauna between islands on either side of the line.

Dipterocarps are predominant trees in the lowland forests of Sundaland. Sundaland has the greatest diversity of Dipterocarp species, with 10 to 14 native genera and approximately 450 native species, including approximately 267 species on Borneo, 155 on the Malay Peninsula, and 106 on Sumatra.

The eastern boundary of central Malesia (area B in map 2) is formed by Lydekker's Line (line 7 in map 2). Central Malesia can be divided into two subareas: the Philippines in the north and Wallacea in the south.

The Philippines form the northern part of central Malesia. Most of the Philippines were never connected to the Asian mainland, and have a largely Asian-derived flora, and a distinct mammalian fauna.