Two PCR-RFLP mitochondrial DNA (mtDNA) markers were developed through the cloning and sequencing of mtDNA from the scallop Pecten maximus, and were used to study genetic differentiation off UK and Atlantic coast populations of this species. Although no distinct pattern of mtDNA haplotype frequencies was apparent and no diagnostic haplotypes were identified for any population, sequence divergence data provided convincing evidence that a P. maximus sample taken from Mulroy Bay, Eire, a semi-enclosed sea lough, was genetically differentiated form all other samples. However, this could not be unequivocally attributed to a restriction in gene flow, as the sample consisted of an ongrown single spatfall, which may not have been representative of the wild population. Despite the inability to separate populations on the basis of haplotype frequency, it was noteworthy that the frequency pattern of the commonest haplotype varied between sampling sites in a manner similar to that of allozyme allele frequencies in Aequipecten opercularis, a scallop species with a similar distribution and life history, for which there is evidence of population subdivision. Pecten maximus from St. Brieuc Bay, reasoned to be a self-recruiting population from reproductive and physiological evidence, could not be separated from other populations using mtDNA markers. Further investigation of this population with alternative markers is warranted.