Ecogeography and sexual dimorphism represent a significant source of phenotypic variation within mammalian species. The skull is a key trait to investigate such issues, especially in mammals, since its size and shape relate to feeding and other functional adaptations. We explored skull variation in three wide-ranging South American marsupial species to determine the impact of sexual and ecogeographical selection. We selected members of the genus Didelphis that are phylogenetically and morphologically very similar: the generalist Didelphis albiventris, the Atlantic forest dweller D. aurita and the Amazonian forest dweller D. marsupialis. By employing geometric morphometrics, we quantified skull shape and size in a sample of 425 wild-caught adult specimens. Species skull shape responds differently to each explanatory variable: skull size, environment and spatial filters (generated by principal coordinates of neighbour spatial matrices). There is a general pattern between sexes with males exhibiting a larger allometric effect on shape than females. Larger individuals are capable of producing higher bite forces, with a relatively wider zygomatic arch. Male opossums fight each other for mating competition, thus explaining the stronger influence of allometry on their skull shape. Where geographical variation is concerned, we noted higher spatial autocorrelation in the skull shape variation of females. Indeed, in all Didelphis species, females are more sedentary while males tend to be more active, moving across longer distances. The environment alone explains 1% or none of skull shape variation in Didelphis species, although it has a greater role when interacting with size and the spatial filters.