Glacial–interglacial cycles of the Quaternary caused severe changes in species distributions across the western Palaearctic. Past barriers changed into suitable habitats, and today’s corridors acted as barriers during the past. These changes have driven species diversification. Darkling beetles of the genus Pimelia have undergone a radiation in the Mediterranean and provide a suitable species-rich model to test for potential effects from climatic and geomorphological changes on the differentiation of species. We sequenced three mitochondrial genes for individuals of the genus Pimelia from the Atlas Mountains and from the Hoggar Mountains in the south and Libya in the east. Our data show ten genetic lineages scattered across the Atlas Mountains and no genetic split between the Atlas Mountains and Hoggar Mountains. Individuals from north-western Libya are assigned with genetic lineages found in the Atlas Mountains. We assume that orographic structures within the Atlas Mountains have driven strong genetic differentiation during glacial periods. In contrast, the lack of genetic differentiation between the Atlas Mountains and Hoggar Mountains in the south, and north-western Libya underline historical gene flow across the Saharan desert. These findings provide another example of the complex biogeography of North Africa and show how climatic and geographical changes underlie current species distributions and may drive diversification.