Two members of the scallop genus Pecten (Bivalvia: Pectinidae) occur in European waters. Pecten maximus is largely an Atlantic species whilst Pecten jacobaeus is almost completely confined to Mediterranean waters despite slight overlap of distributions in the western Mediterranean. Genetic distances between these species were estimated using both allozyme electrophoresis and mitochondrial DNA PCR–RFLP and shown to be of a similar magnitude to intraspecific values, considerably lower than expected for congeneric species. These data are discussed in the light of recognised morphological differences, hybrid rearing trials and previous studies examining genetic distance by allozyme methodologies.