Our study shows that endangered Bechstein’s bats utilise distinct habitats at different stages of their reproductive cycle, a finding that has implications how habitat should be selected for preservation. Using nuclear and
mitochondrial microsatellite DNA markers we compared gene diversity of Bechstein’s bats within breeding colonies and at potential mating sites. Bechstein’s bat is one of the most threatened European bat species. During
summer it depends largely on mature deciduous forests. Females exhibit strict natal philopatry. They form demographically independent breeding colonies comprising maternally closely related bats. Males are solitary. Like other temperate bats, Bechstein’s bats swarm at the end of summer in front of caves. Because the sexes meet
there, such swarming sites are potentially important for gene flow. Our genetic analyses reveal that swarming sites have greater mitochondrial DNA gene diversity than colonies. Furthermore, field data on the phenology and reproductive status of several hundred individuals suggest that Bechstein’s bats mate during swarming. In combination our field and genetic data show that swarming sites provide the opportunity for gene flow among bats originating from different colonies. Therefore, we suggest that swarming sites should be strictly protected to
maintain the observed high levels of gene flow among colonies.