The objective of this study was to assess breeding and dispersal patterns of both males and females in a monogyne (a single queen per colony) population of ants. Monogyny is commonly associated with extensive nuptial flights, presumably leading to considerable gene flow over large areas. Opposite to these expectations we found evidence of both inbreeding and sex-biased gene flow in a monogyne population of Formica exsecta. We found a significant degree of population subdivision at a local scale (within islands) for queens (females heading established colonies) and workers, but not for colony fathers (the males mated to the colony queens). However, we found little evidence of population subdivision at a larger scale (among islands). More conclusive support for sex-biased gene flow comes from the analysis of isolation by distance on the largest island, and from assignment tests revealing differences in female and male philopatry. The genetic similarity between pairs of queens decreased significantly when geographical distance increased, demonstrating limited dispersal and isolation by distance in queens. By contrast, we found no such pattern for colony fathers. Furthermore, a significantly greater fraction of colony queens were assigned as having originated from the population of residence, as compared to colony fathers. Inbreeding coefficients were significantly positive for workers, but not for mother queens. The queen-male relatedness coefficient of 0.23 (regression relatedness) indicates that mating occurs between fairly close relatives. These results suggest that some monogyne species of ants have complex dispersal and mating systems that can result in genetic isolation by distance over small geographical scales. More generally, this study also highlights the importance of identifying the relevant scale in analyses of population structure and dispersal.