The southern rock lizard Australolacerta australis is a rock-dwelling lizard endemic to South Africa. The phylogenetic relationships of this species with other lacertid lizards are still not clear and have never been assessed in any phylogeny of Lacertidae using DNA sequence data. In this study we employed 3 044 base pairs from mitochondrial cytochrome b, 12S and 16S rRNA genes to investigate the phylogenetic position and the evolutionary history of A. australis. We performed phylogenetic analyses under the assumptions of Maximum Likelihood and Bayesian inference and estimated the timing of the cladogenic events related to A. australis by using a relaxed molecular clock method. Our phylogenetic reconstruction clearly placed A. australis within the southern African branch of the tribe Eremiadini including genera Tropidosaura, Meroles, and Pedioplanis. The former genus constitutes with A. australis a clade endemic to southernmost mountains of Africa. The radiation of this southern African clade is estimated to have occurred during the Mid Miocene (14.7–11.5 Mya), and it was likely due to the climate changes that occurred in the South African region at that time.