Myotis planiceps is an insectivorous species with a distinctive flat-headed morphology among Myotis species. Its distribution is restricted to the northeastern Mexico highlands, and uses trees of Yucca carnerosana to roost. The particular ecological and morphological characteristics of this species make it a likely resource-use specialist. We evaluated the morphological specialization of M. planiceps as compared with thirteen American congeners belonging to different dietary categories, using a geometric morphometric protocol and multivariate statistical analyses. We estimated morphological differences across dietary categories, including M. planiceps as a separate group, and evaluated the effect of cranial size and diet on variations in cranial morphology. We found a significant differentiation of this species in all the cranial shape characters, with soft insectivores as the dietary group closest to M. planiceps. Additionally, diet explained similar percentages of shape variance in cranial and mandibular characters, and the highest interaction between diet and cranial size was recorded in the braincase. In general, the smallest sizes and thinner skulls were observed in soft insectivores. Our findings do not support a significant relationship between skull shape characters, described by the first principal component, and hardness of food items, but we found a significant association with the mandible shape. No phylogenetic structure was observed in the residual variance of these models. We found trends of change in cranial morphology associated with specialized habitats, the mandibular characters being more contrasting in the fishing bat M. vivesi, and the braincase morphology being more contrasting in M. planiceps, a species that lives in restricted habitats and probably feeds on soft insects.