Samples of Ostrea edulis were collected during 1999 and 2000 from five sites in Scotland, and from one site each in Northern Ireland, Ireland, France, The Netherlands and Norway. Samples were scored at four microsatellite loci. Mean numbers of alleles per locus varied from 12·6 to 16·6 and observed heterozygosity per locus ranged from 0·801 to 0·845. Samples derived originally from hatchery seed showed significantly fewer alleles per locus and significantly reduced expected heterozygosity compared with wild populations. However, observed heterozygosity did not differ significantly between the two groups. Significant deficiencies of heterozygotes were present at one or more loci in four of the ten populations sampled and a significant excess of heterozygotes was present at one locus in a hatchery-sourced Scottish population. Genetic distance indices revealed that the Norway population was the most distinct from all others and that hatchery-sourced populations were also relatively distinct from other wild populations. However, genetic subdivision was generally low implying high historical ‘migration’ rates for these populations.