Connectivity is a species- and landscape-specific measure that is key to species conservation in fragmented landscapes. However, information on connectivity is often lacking, especially for insects that are known to be severely declining. Patterns of gene flow constitute an indirect measure of functional landscape connectivity. We studied the population genetic structure of the rare digger wasp Bembix rostrata in coastal and inland regions in and near Belgium. The species is restricted to sandy pioneer vegetations for nesting and is well known for its philopatry as it does not easily colonize vacant habitat. It has markedly declined in the last century, especially in the inland region where open sand habitat has decreased in area and became highly fragmented. To assess within and between region connectivity, we used mating system independent population genetic methods suitable for haplodiploid species. Despite B. rostrata being a poor colonizer, gene flow between existing populations appeared not highly restricted. We found more pronounced genetic structure in the small and isolated inland populations as compared to the well-connected coastal region, including a pattern of asymmetrical gene flow from coast to inland. Most likely, demography within different landscape contexts is the main factor explaining the discrepancy in connectivity and asymmetrical gene flow between the different regions. This illustrates the importance of large populations for the species′ metapopulation persistence. Therefore, to improve the conservation status B. rostrata through increased connectivity, large sites with sand dunes need to be preserved or created, especially in landscapes with small and isolated populations.