Abstract Geometric morphometrics was used to investigate the Ethiopian Myomys - Stenocephalemys complex, and to suggest possible explanations for differences in size and shape. The four species of the complex (M. albipes, M. ruppi, S. griseicauda, S. albocaudata) and a Kenyan species, M. fumatus, were studied using Procrustes analysis of three dimensional landmarks collected over the skull. All these species occur in very different habitats, from forests at 1000 m up to the Afro Alpine moorlands above 4000 m. There is a substantial contradiction between phylogenetic relationships based on chromosomal rearrangements and allozymes (two distinct lineages corresponding to the two genera), and mtDNA (Stenocephalemys being paraphyletic). Geometric morphometrics supports the former hypothesis. Partial Least-Squares analysis shows a significant relation between variation in size and shape and altitude, which strongly suggests that adaptation is a major causal factor for divergence in the morphology of the skull. Size increases with altitude, paralleling a clinal change in shape, which involves stenocephaly as characterising the highland species. This shape modification allows the rodents to scan the sky efficiently for birds, which represent the main category of predators in the Afro Alpine moorlands.