The sword razor shell Ensis siliqua (Linnaeus, 1758) is found mainly from Norway to the Atlantic coast of the Iberian Peninsula. It is intensively caught in Europe, being highly appreciated as seafood. To help in its conservation and management, five microsatellite markers were isolated and genetic variation was analyzed in samples from Ireland, Spain, and Portugal. The highly significant differentiation (θ = 0.287, P < 0.001) observed was mainly due to differences between samples from Irish and Iberian Peninsula localities, except Aveiro (its sample resembled the Irish samples, and it may be predominantly self-recruiting). These groups of samples showed significant differences in allelic richness that could be related to harvesting intensity. Moreover, microsatellites detected low but significant differentiation between Iberian localities (Celeiro and Olhão), and Aveiro differed significantly from Strangford Lough. Overall, results suggest that two independently evolving regions exist and that management strategies should be designed for each region.