Human activities affect biodiversity by reducing the area of habitats, altering their shape, and increasing their isolation. Ants are particularly sensitive to habitat fragmentation, as it may locally change abiotic conditions, the availability of food and nest sites, the abundance of mutualists, competitors and predators, and also restrict gene flow between patches. As a result, the genetic population and colony structure of ants is expected to show signs of fragmentation. In the present study, we investigated the impact of fragmentation on the ant Temnothorax crassispinus in 45 forest patches across the Franconian Jura, Germany. Based on 283 colonies, of which 156 were genetically analyzed, we evidenced the presence of two putative distinct genetic clusters in the study area. Both the nest densities and the presence of queen were impacted by the number of adjacent forest patches within 400 m around the focal patch, but neither by patch shape nor patch size. We could not detect any effect of fragmentation on the genetic diversity, probably because the high dispersal abilities of T. crassispinus counterbalance any detrimental genetic consequences of fragmentation. Nevertheless, fragmentation still impacts the species density as well as the social structure of its colonies. Further investigations regarding the drivers of occurrence at a finer spatial scale might clarify the role of edge effects on the occurrence of this species.