Despite being among the largest and most conspicuous geckos across southern and eastern Africa, the toe-padded species of Chondrodactylus have remained one of the most taxonomically difficult groups of African lizards, due chiefly to their overall morphological conservativeness accompanied by high intraspecific variation. Current recognition of taxa is based on recent molecular phylogenetic analyses, but the application of the currently recognized nomina to particular populations has not yet been presented. We present a much-expanded multigene analysis of 234 representatives of the genus Chondrodactylus that supports the recognition of 6 species-level taxa, one without toepads, C. angulifer, as sister to five with pads: C. bibronii, C. turneri, C. laevigatus, C. pulitzerae, and C. fitzsimonsi. In general, the species can be recognized on the basis of the relative size of chin and gular scales, dorsal scalation, and head shape. However, the most widespread species, C. laevigatus is only very subtly distinct from C. turneri, with which it is likely parapatric in East Africa (although western populations of C. laevigatus are unambiguously diagnosable from all other congeners). Intraspecific divergences are high in some of the species. In C. fitzsimonsi there is evidence of shared nuclear haplotypes with C. pulitzerae and potential morphological evidence for hybridization or introgression with C. laevigatus. Chondrodactylus turneri exhibits a mitochondrial gene rearrangement that is unique among all geckos followed by an insertion of roughly 200 base pairs that do not correspond to known sequences. Most Chondrodactylus species are primarily distributed in arid to semiarid southwestern Africa, where as many as 4 species occur in sympatry in northern Namibia. In contrast, C. turneri is limited to the lowlands of the southeast and C. laevigatus follows the “arid-corridor” traversing sub-Saharan Africa southwest to northeast.