The genus Rhoptropus consists of six species of diurnal, chiefly rupicolous, geckos that are endemic to the arid and semi-arid zones of Namibia and southern Angola. Sixteen skeletal and scalation characters and six allozyme characters analysed cladistically yield a single most parsimonious pattern of relationships: ((R. afer, R. bradfieldi) (R. taeniostictus (R. boultoni (R. barnardi, R. biporosus)))). Support for the placement of R. taeniostictus is tenuous because of missing allozyme data, but the remainder of the topology, especially the basal dichotomy, is well supported. Morphological and allozyme data are congruent and a phenetic analysis of genetic distances among the taxa is consistent with the phylogeny. The diversification of the genus probably took place in the Mid- to Late Tertiary and both basal and distal cladogenic events may be related to the evolution of the Namib Desert and movement of the Namib sands. Rates of evolution among the lineages of Rhoptropus appear to be unequal and R. afer, a species largely restricted to horizontal sheet rock habitats, has accumulated a large number of autapomorphic traits.