Neotropical bats evolved a diverse morphology to explore trophic resources and roost. The variation in skull shape in Chiroptera reflects selective pressures or trophic resources and habitat throughout their evolutionary history. The skull shape is generally related to the trophic guild in phyllostomids, but few analyses have included other families. Here, we tested for phylogenetic signal and the influence of diet and foraging strategy on the skull and jaw shape in 17 bat species. Twenty localities were sampled in Bodoquena, central Brazil. In the 2D images, Landmarks and Semilandmarks were located and overlaid, using Generalized Procrustes Analysis. Data on trophic guilds (Animalivores, Frugivores, Nectarivores) and foraging strategy (Clutter Space Passive-Active, Clutter Space Active, and Clutter Space-Passive) were derived from literature. We performed a phylogenetic signal test of the skull and jaw shape based on Brownian Motion and a Phylogenetic Generalized Least Squares to test the effect of diet and foraging strategy. To verify if the groups were statistically significant, we perform a Pairwise test. To visualize the morphological space and the phylogenetic relationships between species, we built a phylomorphospace with Geomorph. Our results show that the skull and jaw shape of species phylogenetically close is similar and was group in the same phylomorphospace. In the pairwise analyses, we found that both diet and foraging strategy influence the cranial shape. Finally, the morphological space showed that frugivorous and nectarivores species were grouped together, but animalivores had greater differentiation in skull morphology. We suggest that species close phylogenetically and similar in diet could coexist because these species have optimal phenotypes for the exploration of resources as the Stenodermatinae subfamily.