Maternity colonies of the communally breeding, nonmigratory Bechstein's bat consist of closely related females that live together with unrelated females, and average colony relatedness is low despite the absence of immigration. We compared the genetic structure of both nuclear and mitochondrial microsatellites in order to quantify sex-specific dispersal rates. More specifically, we aimed at testing whether male dispersal is able to balance the genetic effect of strong (absolute) female philopatry. Absolute female philopatry, indicated by an extreme mitochondrial DNA population differentiation of 96%, was indeed opposed by strong (possibly complete) male dispersal. Based on our knowledge of the biology of Myotis bechsteinii, we conclude that inbreeding avoidance is likely to be the crucial factor driving male dispersal in this species.