||The evolutionary history of the dwarf gecko genus Lygodactylus is analyzed with a focus on southern African representatives. Phylogenetic relationships were inferred from a multilocus dataset of 38 Lygodactylus species including all southern African taxa. This dataset is used to investigate the historical biogeography of the genus, and species limits and patterns of diversification within southern Africa. My results support an 'out-of-Madagascar' hypothesis for the genus, with overseas dispersal across the Mozambique Channel and the Atlantic Ocean fueling the radiation. Within southern Africa they have undergone two extensive radiations, resulting in a savanna and an Afromontane species-complex. I detected extensive paraphyly in the species-groups and non-monophyly of the polytypic southern African species. There are also high levels of cryptic diversity in the widespread capensis -group. The results of this study have taxonomic and conservation implications, and add to the growing body of knowledge on the origin and evolution of African biodiversity.