While the comparative phylogeography of European fauna is relatively well understood, with Pleistocene climatic oscillations leading to ‘southern refugia’ for many species, the equivalent pattern has not been determined for North Africa. In this context variation within North African populations of the riverine snake Natrix maura were assessed using mitochondrial DNA sequences. Recent literature regarding North African phylogeographic studies of reptiles was compiled, and several surprising patterns emerged. The most interesting was the extensive movement of species across the Strait of Gibraltar during the Pleistocene. Another is the general pattern of deep genetic divergences between Tunisian and Moroccan populations, often at a level implying the existence of cryptic species. Natrix maura has three distinct lineages in North Africa, however, it apparently did not cross the Strait of Gibraltar during the Pleistocene, but probably did so during the Messinian salinity crisis.