Microsatellites were used to investigate fine-scale spatial and temporal genetic structure of a gray seal breeding colony, using samples collected throughout the colony (1997) and more extensive local sampling (2000–2002). Previous behavior of breeding seals on North Rona, including philopatry and high breeding site fidelity, suggested female kin may cluster together. However, low FST scores indicated no genetic differentiation between the major breeding aggregations in different regions of the colony. Nevertheless, the pairwise relatedness of mothers within regions was significantly higher than the relatedness of mothers between regions. Evidence of kin clustering occurred within one region in the colony. Within this region, mothers' pairwise relatedness decreased significantly with increasing distance between pupping sites. Pairwise relatedness of neighboring females within this region was also higher than expected. Conversely, in the other regions mothers that were considered likely to have social interactions, based on their spatial and temporal proximity, were not more related to each other than random. Therefore, sustained philopatry appears sufficient to produce differences in relatedness at a within-colony scale (>500 m), but not at finer scales. This suggests that long-term associations of mothers on North Rona detected previously are unlikely to be formed solely by close kin.