||The intraspecific relationships within two lygosomine skink species in southern Africa, Trachylepis sulcata and T. variegata , were analyzed using both tree based and non-tree based molecular methods. The broad range of each species allowed for the investigation of potential biogeographic barriers across Namibia and South Africa. Phylogenies reconstructed from mitochondrial (ND2) and nuclear markers (RAG-1, EXPH5, and KIF24) indicate that both species exhibit high genetic diversity in northern Namibia and low genetic diversity in southern Namibia and South Africa, which is consistent with a historical southward range expansion. Based on a population clustering analysis, the Knersvlakte region in the Northern Province of South Africa was identified as a biogeographic barrier in the rock-dwelling species T. sulcata , but not in the generalist species T. variegata . Additionally, the previously defined subspecies within both species were assessed based on molecular and morphological evidence, with special attention given to the melanistic subspecies, T. s. nigra .