European Council Regulation 104/2000 states that fishery products must be labeled to indicate commercial designation of species, the production method, and the catch area. Therefore, traceability of seafood implies knowledge of the species offered to retail and their origin. Ensis siliqua is a bivalve intensively fished in Europe and sold in fresh and canned forms. Although several published methods clearly differentiate Ensis genus species, none of those assess the origin of the commercial samples. In the present study, a microsatellite marker (Esi-UDC3055F) was developed to establish the catch area of E. siliqua samples. Amplification yielded a fragment of 275 or 302 base pairs, depending on whether they were Iberian or Irish populations. The usefulness of this method was also assessed in commercial samples. The results of this study provide a reliable methodology for the identification of catch area in European E. siliqua commercial samples. The coupling of this methodology with existing techniques for razor clam species identification provides a powerful tool for traceability and labeling enforcement.