An analysis of morphological and allozyme variation in leaf-toed geckos of the Phyllodactylus lineatus complex from southern Africa is presented. Five separately evolving lineages, well-defined by morphology and allozyme variation, are identified, along with another less well-defined isolate. Typical P. lineatus is shown to be a deep-headed, large-scaled, terrestrial species, with usually five preanal pores in males. It is widely distributed in the Succulent Karoo biome, from southern Namibia to Saldanha, and into the western Little Karoo. The remaining populations, containing dorsa-ventrally flattened, rupicolous lizards, are all geographically isolated. Phyllodactylus rupicolus (new comb.) and P. essexi are validated as full species, diagnosed by being small (< 30 mm snout-vent length), having four preanal pores in males, and usually 1–3 nasorostrals. They can be distinguished from each other in morphometric space and by allozymes. Two well-defined populations in the western and southern Cape Fold Mountains, distinguished by allozyme and/or morphological features, are described as new species; P. hexaporus, whose distribution is centred around the Cedarberg and Kouebokkeveld, is characterized by having six preanal pores in males; P. hewitti. distributed in the southern Cape Fold Mountains, is characterized by having only four preanal pores in males, usually only 0–1 nasorostrals, and reaching a maximum snout-vent length of 37 mm. An isolated population on the inland escarpment of the Nuweveldberge, north of Beaufort West, is conservatively referred to the latter species but may also deserve specific recognition; this is withheld pending further allozyme studies.