• colony structure;
  • dispersal;
  • gene flow;
  • microsatellites;
  • relatedness

Although two cryptic pipistrelle bat species, Pipistrellus pipistrellus and Pipistrellus pygmaeus, belong among the most common bat species in Europe, it is still unclear whether they can migrate over long distances between summer and winter roosts. Long-distance migratory species may be expected to show low levels of genetic structuring in large areas due to regular mixing of the gene pool by mating that occurs during migration and/or hibernation. Conversely, the dispersal of gametes in sedentary species is spatially restricted, populations are more genetically structured, and isolation by relatively short distance is visible. By analysing diversity of highly variable microsatellites within and among summer colonies of both studied species in central Europe, we found that differentiation between populations is very weak. Both classical FST and Bayesian clustering approach failed to detect genetic structure among colonies and there was no significant isolation-by-distance pattern. The analyses of relatedness, however, revealed that individuals within colonies are more related than random suggesting philopatry of at least one sex. The results were very similar for the two species. The high level of gene flow among central European populations, even on large geographic distances, is discussed in relation with migrations, dispersal, and mating behaviour. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 103–114.