The present study aims to depict the overall pattern of the history of the North African dipodil, Gerbillus campestris, in the northern Sahara. More specifically we document whether or not Pleistocene refugia, the Sahara desert, and the Moulouya River structure patterns of diversity in this species. The phylogenetic relationships among populations were determined by analyses of the cytochrome-b gene in 100 specimens collected in 5 countries (Morocco, Algeria, Tunisia, Mali, and Niger) and 27 localities. Our study highlights a complex phylogeographic pattern for G. campestris in North Africa, with 9 phylogenetic lineages differing by up to 2.5% of sequence divergence. Most of these lineages are allopatric, except in Morocco where 2 lineages are overlapping in the south. These genetic lineages probably arose during the successive cycles of cooling and warming climatic conditions that characterized the end of the Pleistocene, caused by the combined effects of habitat changes and marine transgressions. The divergence between Saharan and Moroccan populations occurred during a period of aridification at the end of the Pleistocene. The Moulouya and the Bou Regreg rivers also seem to be major biogeographical barriers to gene flow in this species.