Schotia has a southern African distribution with a strong affinity to the thicket biome and is a potential indicator of thicket biogeography. This study uses DNA sequence data (from the chloroplast and nuclear genomes) to infer interspecific phylogenetic relationships, to elucidate the evolutionary history of Schotia, and to extrapolate findings to the history of the thicket biome. Four species of Schotia represented by multiple samples were nonmonophyletic for both chloroplast and nuclear markers. These results may be due to hybridization and/or incomplete lineage sorting, which also suggests a recent origin of Schotia morphospecies. The center of genetic and taxonomic diversity of Schotia is the Eastern Cape and partly the Western Cape, coinciding with the hub of present‐day thicket distribution. This region is hypothesized as being a refugial area for Schotia (and the associated thicket biome) during glacial periods, with expansion beyond this region during interglacial periods. Keywords: cpDNA, Fabaceae, ITS, Leguminosae, phylogeography, Schotia, southern Africa, thicket biome.