Abstract Three-dimensional geometric morphometrics was used to investigate patterns of growth and differences in size and shape of the skull of three species of the African rodent genus Lophuromys, representing the two subgenera Lophuromys s.s. (represented by a population of L. flavopunctatus from Rwanda and a population of L. sikapusi from Ivory Coast) and Kivumys (represented by a population of L. woosnami from Rwanda). Procrustes superimposition was used to study variation in 21 three-dimensional landmarks. Differences in shape were visualised by using current available graphical morphometric techniques. Significant differences in centroid size were found both between species, sexes, and age classes. The pattern of growth in size is parallel between species, suggesting that it has been maintained after cladogenesis. No significant sexual dimorphism in shape has been found. Moreover, growth significantly affects the shape of the skull of L. flavopunctatus, but not that of L. sikapusi and L. woosnami. The main distinction in shape reflects thc phylogenetic occurrence of the two subgenera, i.e. Kivumis and Lophuromys s.s. However, the knowledge on the biology of these species is inadequate to exclude that any other adaptive factor (e.g. diet, climate, etc.) may have contributed in causing shape differences.