The great scallop Pecten maximus (Bivalvia: Pectinidae) supports a substantial European fishery with a recent history of declining catches caused by over-exploitation. The sustainable exploitation of shellfish populations requires knowledge of the extent to which commercial grounds are reproductively self-sustaining or supplied with larvae originating from further afield. The degree of genetic differentiation between locations can provide important indirect evidence, reflecting the pattern and scale of effective larval dispersal. Pecten maximus were sampled from five locations around the Isle of Man, from Mulroy Bay (Ireland) and from Plymouth. Restriction-site variation was investigated in two PCR-amplified mitochondrial DNA fragments of 2 and 3 kb, respectively. Haplotype and nucleotide diversity within populations, and nucleotide divergence between populations, were calculated. Mean nucleotide sequence divergence was corrected for within-population polymorphisms and visualized by UPGMA cluster diagrams. Molecular analysis of variance (AMOVA) was carried out. Results showed low levels of population differentiation. Slight but significant differentiation between Isle of Man populations was revealed, with East Douglas appearing distinct from the remaining Manx locations. The analyses also indicated the distinction of Mulroy Bay from the other populations, and the lowest genetic variability was recorded from this enclosed habitat. This probably reflects the relative isolation of Mulroy Bay, whereas dynamic hydrographic conditions in the Irish Sea and the Channel may generally ensure extensive mixing of the planktonic larvae.