The Southern African biomes are complex biotic communities, with its distinctive plant and animal species, and are maintained under the suitable climatic conditions of the region. It includes the Fynbos Biome and the Succulent Karoo Biome, which forms the smallest of the world’s six Floristic Kingdoms, and they are of conservation concern. The other six biomes are Albany Thicket, Desert, Grassland, Indian Ocean Coastal belt, Nama-Karoo, Savanna. The biomes are not only threatened by agricultural expansion, overgrazing, and mining; but also by future climate changes and droughts. This study investigates the how to best model the possible vulnerable biome areas, under future climate changes, and how Southern African geology plays a huge role in the restriction of the biome shifts. It provides evidence regarding the importance of the study to understanding the climate change impacts and the geological variables on the Southern African biomes, in terms of possible future biome habitat loss.