Species in genus Myotis exhibit a pattern of cranial variation associated with insectivorous, facultative piscivorous, and truly piscivorous diets, which has not been studied in a phylogenetic context. Variation in landmark configurations of five cranial structures in 22 Myotis species was analyzed with phylogenetic methods to infer evolution of shape. Our goals were to detect changes in cranial morphology and to correlate these with concerted changes among diets. A reference phylogeny was estimated using a combined data matrix with previously available Cyt-b and RAG2 sequences and our five configurations of landmarks. We included the insectivorous Kerivoula papillosa Temminck, 1840, Noctilio leporinus Linnaeus, 1758 (piscivorous), and N. albiventris Desmarest, 1818 (insectivorous) as out-groups. The optimization of five landmark configurations on the combined phylogeny shows no evidence of convergent shape changes among species with similar piscivorous diets. Our findings document that facultative piscivory does not imply the same particular morphotype. In four cranial features, there is small shape change between estimated ancestral shapes and seven observed descendant shapes for the piscivorous species. Only the mandible shows major changes from insectivorous ancestors to facultative piscivorous or piscivorous Myotis.