Maternity colonies of the Bechstein’s bat (Myotis bechsteinii) are socially closed units that frequently split into subgroups which occupy different roosts. We analysed the social structure of one colony over three years in the field and quantified associations among pairs of females by using three association indices. Colony members exhibited marked mixing, although individual composition of subgroups was not completely random. Females associated according to the reproductive status, with lactating females preferentially roosting together. Relatedness, determined from 5 nuclear and 1 mitochondrial microsatellite, had no consistent influence on the degree of association. In combination, the indices allowed for the interpretation that nonrandom associations occur even in the absence of shared roost and group size preferences. High individual associations among reproducing female Bechstein’s bats might reflect the importance of cooperation in maternity colonies. The frequent fission and fusion of subgroups suggests a flexible reaction of Bechstein’s bats according to enviromental conditions.