We examined phylogenetic relationships among the Namib day geckos (genus Rhoptropus) using DNA sequence data from the mitochondrial cytochrome b (cytb) and 16S ribosomal RNA genes. Maximum-parsimony analysis of the cytb, 16S, and combined (cytb/16S) datasets each recovered an identical single most-parsimonious tree, revealing two well-supported clades: (1) Rhoptropus afer + Rhoptropus bradfieldi ssp and (2) Rhoptropus boultoni + (Rhoptropus barnardi + Rhoptropus biporosus). Maximum-likelihood analysis identified the same two species groups and corroborated patterns of relationship within respective parsimony clades. Moreover, the mitochondrial DNA trees were congruent with parsimony trees derived from morphological and allozymic characters. Congruence observed among these different data offers strong evidence for our molecular phylogeny of Rhoptropus, bringing taxonomic stability to a genus whose species-level relationships were widely debated throughout the last century.