| Summary: | Large hibernating aggregations and behaviour called late summer or autumn “invasions” when large groups of bats enter buildings are known in pipistrelles. We investigated differences in roosting behaviour between two cryptic species (common pipistrelle, Pipistrellus pipistrellus, and soprano pipistrelle, Pipistrellus pygmaeus) during autumn and winter periods. In total 463 bats were sampled in both caves and buildings with temporary occurrence during the period of late summer and autumn mating and presumable migrations from late July to September (10 sites), and in all known types of hibernacula from late November to March (34 sites). Sampling sites were located within the Czech Republic, Slovakia, Serbia and Romania in areas where the two species occur sympatrically throughout the summer. Using a DNA-based identifi cation method, all but four individuals were identifi ed as P. pipistrellus. It means that winter roosts of P. pygmaeus remain largely unknown in the area. Similarly, no P. pygmaeus was found in the “invasion” assemblages. Very abundant groups of P. pipistrellus in underground hibernacula and its exclusive occurrence in sites of “invasions” suggest that roosting behaviour during this time may be species-specifi c.
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