Geographical genetic population structure was determined for an endemic African leporid, Smith's red rock rabbit, Pronolagus rupestris. Restriction fragment length polymorphism analysis of mitochondrial DNA from 55 specimens revealed 32 distinct material lineages for the population sampled. The data show two major genetic assemblages separated by a mean sequence divergence of 7.94 per cent (+/- 1.40 per cent) and provide little support for the continued recognition of most of the described subspecies. The south-eastern assemblage is confined to the mountain ranges comprising the Great Escarpment of South Africa, while the north-western assemblage is not so tightly constrained. With the possible exception of elevation, no readily apparent ecological or topographical barrier could be identified which delimits the two mitochondrial clades. The sequence divergence separating the south-eastern and north western P. rupestris clades is high, and approximates the interspecific sequence divergences detected between P. rupestris and other Pronolagus species. The two P. rupestris clades are parapatric for part of their distribution, and the absence of shared mtDNA lineages is consistent with the hypothesis that the two populations are reproductively isolated from each other. We provisionally interpret this to reflect the presence of two hitherto undetected biological species in what has conventionally been recognized as a single taxon, P. rupestris.