Roost fidelity is an important aspect of mammalian biology. Studying the mechanisms underlying philopatry can help us understand a species’ energetic requirements, ecological constraints and social organisation. Temperate bat species notably exhibit a high degree of female philopatry considering their size, resulting in maternity colonies segregated at the mitochondrial level. We focus on the greater noctule, Nyctalus lasiopterus, to study this behaviour in more depth. We make use of microsatellite data for 11 markers across 84 individuals residing in Maria Luisa Park in Seville, Spain. At the time of sampling this urban park boasted the highest number of bats of any known colony of this species, among which three social groups were observed to segregate spatially. We studied the distribution of pairs of individuals across filial relationship categories and relatedness estimates relative to the social group of each individual. This analysis was complemented by information on roost-use frequency among a subset of genotyped bats. We found no significant relationship between roost use and genetic distance, but there was evidence that more closely related bats are more likely to be found in the same social group. Mother-daughter pairs shared the same group more often than expected, as did pairs of individuals of relatedness above 0.43. We discuss the implications of these results in terms of the behavioural ecology of temperate bats and for conservation efforts aimed at preserving them.