Using museum collections and recently collected specimens we studied geographical and temporal (from 1906 to 2013) changes in skull size of two sibling species of rodents, Otomys auratus and O. angoniensis, in northern South Africa occupying distinct temperate grassland (O. auratus) and subtropical savanna (O. angoniensis) biomes. We hypothesised that cranial size should vary in space and time within species according to Bergmann’s Rule, which predicts an inverse relationship between body size and temperature. We used the greatest length of the skull (GLS) as a robust indicator of body size. Cranial size of both O. auratus and O. angoniensis decreased significantly over the past 100 years, as expected given historical evidence of warming across northern South Africa since the 1950s. In terms of geographical patterns, GLS was inversely correlated with both latitude and longitude in O. auratus but these trends were correlated with annual rainfall rather than mean annual temperature. Conversely, cranial size of O. angoniensis was weakly positively correlated with longitude but with no climatic variables. Our results demonstrate rapid morphological changes in two herbivorous South African rodents over the past 100 years. Whilst the general decline in size with time in relation to increased temperature is consistent with Bergmann’s Rule, multiple drivers may underlie geographical trends in the two species.