Management of commercial fisheries resources is commonly done assuming that populations are spatially homogeneous throughout their geographic range. However, uneven gene flow can result in gradients of genetic diversity that can affect population dynamics and management reference points and may contribute to overfishing. We examined whether the brown swimming crab, Callinectes bellicosus, fished along 1200 km on the coast of Sonora (Mexico) is a homogeneous population. Based on previous empirical evidence of differences in phenology, we hypothesized that C. bellicosus has a metapopulation structure which needs to be included in management tools. We conducted a genetic study of C. bellicosus taken at seven sites along the coast of Sonora and obtained their microsatellite genotypes. Recent gene flow, as well as the role of each site as source or sink, were investigated. We found a latitudinal gradient in genetic diversity and identified sites along the coast acting as sources or sinks of migrants. Central sites act as sources, while northern sites are sinks; the main source of migrants was the southern-most site. A predominantly asymmetric metapopulation structure composed of local populations with moderate connectivity may be explained by larval dispersal in the northward oceanic current during the spawning period. Including migration rates between sites in a metapopulation dynamics model of C. bellicosus and considering that fishing and management decisions in source populations will impact neighboring populations located downstream can improve current management of this important commercial fishery.