A hypervariable simple sequence locus and mitochondrial D-loop sequences were used to analyse genetically a natural population of the larger mouse-eared bat Myotis myotis in southern Bavaria. Tests for population subdivision and direct observations suggest that females return to their natal sites, while males disperse. The males present in female nursery colonies are not related to the females. Paternity assessment for 46 offspring from a particular nursery colony showed that there are no males that monopolize the reproduction, and that the resident males in the colony had only a small mating success. Instead, the results suggest that females actively seek matings outside their colony. Most interestingly, it appears that a group of males about 16 km away from the nursery colony had a relatively high mating success and that this group of males may be related to the females of the nursery colonies. If this finding can be confirmed in a larger study, it may have important consequences for future conservation strategies.