Quaternary climatic oscillations and geographic barriers have strongly influenced the distribution and diversification of thermophilic species occurring in the Mediterranean Basin. The Western Mediterranean pond turtle, Mauremys leprosa, is widely distributed throughout the Iberian Peninsula, southern France and most of the Maghreb region, with two subspecies currently recognized. In this work, we used 566 samples, including 259 new individuals, across the species range, and sequenced two mitochondrial markers (cytochrome b gene and control region; 163 samples in a concatenated mtDNA dataset) and one nuclear intron (R35; 23 samples representing all identified sublineages) to study the evolutionary history of M. leprosa. We combined phylogenetic methods and phylogeographic continuous diffusion models with spatial analysis. Our results (1) show a high level of genetic structure in Morocco originated during the Pleistocene; (2) reveal two independent population expansion waves from Morocco to Tunisia and to southern Europe, which later expanded throughout the Iberian Peninsula, and (3) identify several secondary contact zones in Morocco. Our study also sheds new light on the role of geographical features (Moroccan mountains ranges and the Strait of Gibraltar) and Pleistocene climatic oscillations in shaping genetic diversity and structure of M. leprosa, and underlines the importance of the Maghreb as a differentiation centre harbouring distinct glacial refugia.