In this study, we investigate skull size and shape differentiation between sibling species of Mastomys with the aim to characterize and discriminate three sympatric species found in West Africa: M. huberti, M. erythroleucus and M. natalensis. A total of 133 genetically determined specimens were used for the morphometric analyses. Statistical analyses clearly demonstrated that the three species largely overlapped in centroid size (M. erythroleucus tends to be larger on average than the M. huberti and M. natalensis) but they exhibited large differences in skull shape. The current study focused on skull shape, and allowed us to discriminate three morphological groups that are congruent with the three species suggested by molecular identification (90% of the individuals are correctly assigned by cross-validated classifications). In the Mastomys, the evolution of cranial length and shape may be influenced by competitive pressure between closely related species separated by ecological segregation. This source of variability could possibly induce character displacement between species of Mastomys.