This study uses geometric morphometric techniques to examine cranial size and shape variation in nine isolated populations of the tammar wallaby (Macropus eugenii). A set of 36 three-dimensional landmarks were digitised on 143 tammar crania from two mainland and seven island populations. While there was no evidence of island dwarfism or gigantism, cranial size increased with both increasing island size and increasing latitude. As latitude increased, the palate narrowed relative to the nasal bones, cranial flexion and nasal height increased, and the zygomatic arches spread out laterally from the cranium. Overall, the anterior nasal aperture (nares) narrowed with increasing latitude. Mean shapes were calculated for each population, and pair-wise comparisons were made; most of these were significantly different. There was a clear tendency for island populations and those with greater geographic separation to show greater shape differentiation. Thus, regional and population differences in the cranial size and shape of tammar wallabies provide examples of selection, founder effect and random genetic drift.