Long-term trends in climate, hydrology and geomorphology contributed to the formation of the current biomes of southern Africa. The Neogene terrestrial fossil record is patchy, due to the geomorphological evolution of the subcontinent and the restricted distribution of suitable sediment deposits. Here we review the hypotheses on the evolution of the topography and environment and concentrate on the fossil record, especially pollen, wood, charcoal, leaves and biomarkers. Tectonic studies suggest a lower relief landscape than at present at the onset of the Neogene. Southern Africa was drained by two river systems – the Kalahari and the Karoo Rivers – and was affected by an initially weak, cool Benguela current along the western coastline, gradually promoting an aridity trend along the southwestern coast. The Cape region during the Miocene, when the Great Escarpment began to evolve, was characterised by humid, subtropical forests not unlike those still occurring on the much wetter subtropical eastern shore of southern Africa. Southern Namibia (Sperrgebiet) was probably covered by a "proto-savanna"; hyper-aridity developed further north along the Namibian coast. Probably with more uplift, the hydrological regime changed c. 15 Ma when the palaeo Karoo and Koa Rivers were captured by the Kalahari/Orange River and drained western South Africa. Miocene fossil sites are missing in southeastern Africa. In southwestern Africa an enhanced aridity trend and the shift to a winter rainfall regime during the late Miocene-Pliocene was triggered by the development of the Westerly wind system and further strengthening of the cold Benguela current enhanced by the development of the Antarctic sheet and opening of the Drake passage. Eastern southern Africa was dominated by the Great Escarpment and relatively shorter deeply incised rivers and higher rainfall than the west. The Pliocene saw the evolution of the Fynbos and Succulent Karoo biomes including the further radiation of several drought adapted plant families encompassing the Asteraceae and Aizoaceae. At the transition towards the Pleistocene, the region around Sterkfontein in eastern central southern Africa, important for hominid evolution, experienced a shift from a woody environment towards more xeric, open conditions. The Savanna biome today stretches from northeastern South Africa as far north as East Africa; the Grassland and Fynbos biomes are unique and the more arid biomes are dominant in the western half of southern Africa. Keywords: Neogene, biomes, vegetation history, southern Africa.