A recent molecular-based study suggested that two sister species of mouse-eared bats (Myotis myotis and M. oxygnathus) share some mtDNA haplotypes when they occur in sympatry. We used traditional morphometric methods in order to find potential hybrid specimens. Multivariate morphometric analysis of 22 cranial and dental characters was applied to a sample of 298 adult specimens of mouse-eared bats (Myotis myotis and M. oxygnathus) from their sympatric range in the Carpathian Basin. Additionally, we included several juvenile exemplars of both species in order to exclude the treatment of juvenile specimens as individuals with intermediate characteristics. Principal Component Analyses (PCA) and Discriminant Function Analysis (DFA) revealed a distinct separation between specimens of M. myotis and M. oxygnathus, with 6 specimens in an intermediate position. All intermediate specimens come from the contact area of M. myotis and M. oxygnathus. A subsequent detailed analysis showed that intermediate specimens are similar to M. myotis in skull and mandible size, but with tooth-row size similar to M. oxygnathus. An analogous situation has been described in several species of small mammals. Bats designated as intermediate are probable hybrids, i.e. their phenotypes lay between the parental forms.