Geometric morphometrics is a powerful tool for the study of morphological variation that possesses numerous advantages over the more traditional approach based on linear measurements. We analyzed skull morphology, comparing traditional with geometric morphometrics, of 3 different developmental pathways in Mastomys natalensis (Rodentia: Muridae) from a single population. During early development growth patterns were influenced by environmental factors, specifically rainfall pattern, consistent with previous reports that growth trajectories vary according to the amount and distribution of rain. Results confirmed that early growth rate is one of the main determinants of size and shape differences in the skull in the 3 developmental pathways (generation types) of M. natalensis. Other factors, such as food quality and consistency, also could play an important role. Overall, geometric morphometrics appeared more sensitive than the traditional method in detecting variation in skull morphology, but both approaches led to very comparable conclusions. Phenotypic plasticity is an alternative explanation to local adaptations for ecogeographical morphological variation.