Geology provides the basis for understanding distributions of faunas and floras in Southeast Asia but only via a complex interplay of plate movements, palaeogeography, ocean circulation and climate. Southeast Asia grew incrementally by the addition of continental fragments, mainly rifted from Australia, and added to the margins of Sundaland as a result of subduction. Sundaland was an almost permanent land area from the beginning of the Mesozoic. The addition of the continental fragments of Southwest Borneo and later East Java–West Sulawesi formed a much larger emergent land area by the Late Cretaceous that extended from Indochina to West Sulawesi. Subduction resumed at the Sundaland margin in the Eocene and this led to widespread rifting within Sundaland, and formed one of the most important barriers at its edge, the Makassar Straits. Australia began to collide with Southeast Asia about 25 million years ago, effectively closing the former deep ocean separating the two continents, and forming the region now known as Wallacea. Collision, volcanism, and subduction-related processes have led to rise of mountains but also formed new oceans within this complex region. Plate tectonic movements and collisions were intimately linked to changing topography, bathymetry and land/sea distributions which have in turn influenced oceanic circulation and climate. As the deep-water barrier between Australia and Southeast Asia was eliminated and mountains rose, deep marine basins also formed. Eustatic changes in sea level further contributed to a complex palaeogeography. The present gateway between the Pacific and Indian Oceans is the only low latitude oceanic passage between the world’s oceans, and is an important influence on local and probably global climate. The gateway is likely to have been just as significant in the past. Understanding the geology, then palaeogeography, and then their oceanic and climatic consequences are vital steps on the way to interpreting present distributions of plants and animals.