AbstractAimTo assess if geographical and/or environmental factors are driving skull morphology and genetic structure in the cosmopolitan bat species, Tadarida brasiliensis.LocationNorth, Central and South America, Greater and Lesser Antilles.MethodsWe analysed morphometric, genetic and environmental data from the entire distribution of T. brasiliensis. Individuals were genotyped at nine nuclear loci, and clustering analyses were used to detect genetic groups and test correlations between genetic, geographical, and environmental distances. Museum specimens were photographed and 111 two‐dimensional landmarks were digitized per individual. Multivariate analyses were applied to explore whether factors such as sex, genetic group, subspecies, biogeographical regions, latitude, longitude and/or environment contribute to the morphometric variation of this species. We also applied a novel approach based on trend surface analyses and model selection to compare models of spatial and environmental dependence and to predict size, shape, and allometry‐free variation across the Americas.ResultsGenetic and morphometric differences among populations coincide with major biogeographical and climatic breaks in Nearctic, Neotropical and Antillean regions. Trend surface analyses showed that skull size variation can be explained by spatial factors (latitude and longitude), whereas skull shape can be explained by the interaction of spatial and environmental factors. However, allometry‐free shape variation might respond to complex interactions not captured by our models.Main conclusionOur explicit testing of spatial and environmental dependence using geostatistical model selection approaches allowed us to identify extrinsic factors that shape genetic and phenotypic responses in a cosmopolitan bat species. Our findings suggest that skull size is primarily driven by geographical factors (genetic drift), whereas shape variation is driven by adaptive responses to environmental conditions.