In the present study the evolutionary relationships among Cordylusniger–oelofseni–cordylus are investigated using molecular sequence data to: (1) estimate the divergence within this group; (2) date the origin of melanism in the clade and to evaluate possible palaeoecological events responsible for its evolution; (3) examine the systematic relationships among the three isolated populations of C. oelofseni that were previously shown to be polyphyletic using allozyme data. The recovered topology for the combined sequence data (16S and NADH dehydrogenase component 2 (ND2)) among C. niger–oelofseni–cordylus suggests that melanism evolved only once in the clade. The application of a molecular clock to the data demonstrates that melanism evolved during the Miocene epoch, 17–15 million years ago. We believe that the development of a cold-water current and upwelling system along the south-west coast of Africa during this epoch was instrumental in the evolution of melanism in this lizard clade and possibly also in other ectotherm clades with melanistic forms occurring in the area. The results show that C. oelofseni, as presently construed, is composed of three distinct evolutionary lineages, with no shared haplotypes present and marked sequence divergence. Two of the three lineages represent undescribed species. Cordylus cordylus is composed of two distinct clades, a montane clade and a coastal lowland clade. Cladogenic activity in mountain areas of the Western Cape in South Africa has been particularly pronounced and the systematic diversity of many taxa may have been underestimated.