We assessed parentage within and among maternity colonies of northern long-eared bats (Myotis septentrionalis (Trouessart, 1897)) in north-central Kentucky, USA, from 2011 to 2013 to examine colony social structure, formation, and membership dynamics. We intensively sampled colonies in close and remote (>10 km) proximity before and after targeted day-roost removal. Colonies were not necessarily composed of closely related individuals, although natal philopatry was common. Adjacent colonies often contained maternally related individuals, indicating that some pups did disperse, albeit not far from their natal home range. Whereas some young had been sired by males also collected on site, most had not, as would be expected since the species mates in fall near hibernacula across a wider landscape. The number of parentages that we inferred among colonies, however, suggests that outside the maternity season, social groups may be relatively flexible and open. Analysis of microsatellite DNA data showed a low FST(0.011) and best fit to a model of one multilocus genotypic cluster across the study area. We observed high turnover in colony membership between years in all colonies, regardless of roost-removal treatment. Our results suggest that female northern long-eared bats exhibit fidelity to a general geographic area and complex, dynamic social–genetic structure.