We examined phylogenetic relationships of the Pachydactylus rugosus complex using DNA sequence data from segments of the mitochondrial genes cytochrome b and 16S ribosomal RNA. These molecular data support the contention that members of the rugosus complex, as defined by McLachlan (1979), form a monophyletic group. Further, high levels of sequence divergence observed between currently recognized subspecies (19.1-26.8 % for cytb), even across short geographic distances, support elevation of each member to full specific rank. The pattern of relationship within the P. rugosus complex species is P. rugosus (P. barnardi, P. formosus). Sequence data provide no evidence to support a close relationship between these taxa and P. capensis, to which previous workers had assigned both P. formosus and P. barnardi. Keywords: 16S ribosomal RNA, Cytochrome b, DNA, Mitochondrial genes and Phylogeny.