Extensive colour pattern variation in Namibian populations of geckos of the Pachydactylus punctatus complex is geographically consistent and is corroborated by minor, but statistically significant, differences in scalation and body proportions. Canonical discriminant analysis and colour pattern support the recognition of two species in the complex, P. punctatus Peters 1854, distributed throughout southern Africa east of the Western Escarpment in Namibia, and P. scherzi Mertens 1954, restricted to western Namibia, north of the Kuiseb River. Regional colour variation occurs in each species, but current evidence does not support the formal taxonomic recognition of subspecific groupings. Keywords: Reptilia, Gekkonidae, Pachydactylus, Namibia, systematics, variation, zoogeography.