The great scallop Pecten maximus is harvested in several European countries and fisheries targeting this species are severely regulated by fishing quotas. In addition, hatchery-based population enhancement has been developed in some countries to provide alternative or complementary production. The genetic structure of wild populations of P. maximus and the potential impact of aquaculture on the genetic diversity of this species remains poorly documented. In this study, we explored the genetic structure of P. maximus using 12 microsatellite markers, considering 14 populations sampled from Galicia (Spain) to the North of Norway, and one population of Pecten jacobaeus (L., 1758) from the Lion Gulf (Mediterranean Sea). Results indicated a clear differentiation between Norwegian and Atlantic (from Ireland to Spain) populations, but very little to no difference between populations within these two groups. A decrease of the genetic diversity was observed with latitude. No significant reduction of the genetic diversity was observed in the Bay of Brest, where hatchery-based population enhancement has been performed intensively since 1983. Our results are discussed in the light of the inferred recent evolutionary history, phylogeography and connectivity of populations in Europe, and of the phenotypic variability reported in previous studies between northern and southern populations.