Although considerable evidence exists to suggest that certain populations of scallops, Pecten maximus (L. ) are reproductively isolated, attempts to date to differentiate populations using data from allozyme electrophoresis have been unsuccessful. In order to further investigate the population structure of this species, genetic differentiation was quantified using mitochondrial DNA (mtDNA) markers and the results compared to morphological comparisons and allozyme variation. A multivariate morphological study revealed little variation in shell shape although animals from Brest and La Trinite (Brittany, France) appeared to have longer hinges. A population from Saint Brieuc Bay, Brittany which exhibits differences in reproductive cycle from neighbouring populations could not be separated on the basis of shell shape although unquantified differences in shell colour were noted. Allele frequencies at 7 loci assessed by allozyme electrophoresis were essentially homogeneous throughout the sample range in accord with previous studies and provided little evidence for population subdivision. Length variation of the mtDNA was extensive, therefore variability was assessed through a PCR approach in order that this did not cause analytical problems. On the basis of sequence divergence data there was convincing evidence that P. maximus from Mulroy Bay, Eire, a semi-enclosed sea lough, were genetically differentiated from all other samples. This could not be unequivocally attributed to a reduction in gene flow since the sample consisted of an ongrown single spatfall. Although no distinct pattern of mtDNA haplotype frequencies was apparent, the frequency of the commonest haplotype varied between sites with a pattern 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 considerable population subdivision. In comparisons of P. maximus and the closely related P. jacobaeus no consistent differences were detected in morphology, allozymes or mtDNA data. The taxonomic standing of P. jacobaeus is brought into question.