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The spatial genetic structure of a species, and whether distinct genetic lineages are present, is strongly influenced by their biology and habitat requirements. Given habitat specificity and low vagility, many herpetofaunal species are reservoirs for high levels of cryptic diversity; chameleons are a case in hand. The common flap-necked chameleon Chamaeleo dilepishas a large range that spans much of sub-Saharan Africa. Within South Africa, the species is largely confined to the north-eastern and central areas of the country, and occurs from the coastal forests in southern KwaZulu-Natal westwards into Namibia. Their large range, together with anecdotal evidence that there is considerable morphological and phenotypic diversity across the range, suggests a questionable taxonomy with possible cryptic lineages. The aims of the present study were to investigate whether C. dilepisis genetically structured across parts of its South African range, and whether this species (as it currently stands) might include cryptic lineages. To this end, 72 C. dilepisindividuals sampled from four localities across South Africa (Gauteng, n= 2; KwaZulu-Natal, n= 2) were sequenced for two mitochondrial markers (ND4 and 16S). The phylogenetic results suggest that C. dilepisis indeed spatially structured. In addition, the large sequence divergence values between groups strongly suggests the presence of cryptic lineages and, pending the inclusion of more data from a larger geographic range, the group may be in need of a taxonomic revision.