Here we aim to define how skull morphology in an endemic and monophyletic clade of rodents (subfamily Nesomyinae), which show considerable morphological variation and are largely forest-dwelling, has evolved and to characterize this disparity in a geographical and ecological context. We performed a two-dimensional geometric morphometric analysis on 419 dorsal and 444 ventral skull images comprising all nine extant endemic genera (26 different species) and tested the influence of ecological parameters in a phylogenetic context on size and morphology.