Two species of mice inhabit Morocco today: Mus spretus is characteristics of West-Mediterranean undisturbed areas, whereas the cosmopolitan Mus musculus domesticus is typical for anthropogenic habitats. Little is known about the temporal dynamics of interaction between these species in North Africa, mainly because of the difficulty to distinguish them in fossil assemblages, and because of the rarity of detailed analyses of the local fossil record. To tackle this question, we studied morphological variations in the fossil mice from El Harhoura 2 cave (Rabat-Témara, Morocco) using geometric morphometrics. Size and shape of the first upper and lower molars were quantified using a Fourier analysis of their outline. This approach has been proven efficient to discriminate between rodent species or populations. Modern (M. spretus, M. m. domesticus) and extinct Pleistocene species (M. haouzi, M. hamidae, M. jotterandi) from Morocco were used as reference. Our morphometric results evidenced a good discrimination between the Mus species used as reference. This allowed a refined interpretation of the mouse fossil record through the El Harhoura 2 section, ranging from the Late Pleistocene to the Middle Holocene. Most teeth from El Harhoura 2 appeared as morphologically close to M. spretus. It seems that only one species occurred all along the record, attributed to an archaic form of M. spretus. Yet, differences between archaeological levels suggest the occurrence of local evolutionary processes within this species.