We report the first evaluation of mandibular and cranial modularity in the greater horseshoe bat (Rhinolophus ferrumequinum). Although some authors found no modular pattern of these morphological structures in mammals, we discovered that traits integration in R. ferrumequinum is not uniform throughout the mandible and cranium, but structured into two distinct modules. Allometry does not affect mandibular and cranial modularity in R. ferrumequinum probably as a result of the low fraction of shape variation explained by size. Observed at the static level, mandible and cranium modularity in this species could be either functional or developmental or both, but we cannot rule out a genetic nature for underlying mandibular and cranial trait interactions. Evolutionary modularity among related taxa is influenced by genetic and functional modularity. Therefore, future studies on cranial integration and modularity at multiple levels of variation may shed more light on these important features of morphological variability in bats, including R. ferrumequinum.