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Social groups of bats that operate under fission–fusion dynamics tend to establish and maintain non-random associations. We examined the social and genetic structure of the Leisler’s bat (Nyctalus leisleri), a species that is typical of tree-dwelling and long-distance migratory species in Europe. We used long-term co-occurrence data (capture-recapture sampling of roosting individuals) in combination with individual genetic relatedness (inferred from a set of microsatellite markers) to assess relationships between structural, temporal and genetic properties of roosting groups. Our results showed that social structure in groups of roosting Leisler’s bat was not random. Social clusters revealed by network analysis were almost identical to demographic cohorts, which indicates that Leisler’s bats are able to maintain social bonds only over a single season. After the period of active maternal care, roosting groups became smaller with a significantly higher level of genetic relatedness among adult females in contrast to the pregnancy and lactation stages. This provides some evidence that temporal social associations may be positively correlated with genetic relatedness. Low recapture rates of bats across seasons in light of natal philopatry indicates a shorter life span of individuals likely due to high mortality during long distance migratory movements. This probably has the most significant effect on the social system of this species.