We report the isolation, development and multiplex optimisation of 12 new microsatellite loci for the great scallop, Pecten maximus. Diversity was moderate to high, with number of alleles ranging from 4 to 20 and observed heterozygosity between 0.28 and 0.88. Progeny produced in a commercial hatchery was used to test locus power for parentage assignment. The percentage of offspring that was unambiguously assigned to a unique pair of parents was 97% (software package CERVUS-COLONY). Parentage assignment revealed that 22% of the studied progeny resulted from unplanned crosses. Effective population size of the study progeny was also estimated. Our study illustrates the power of microsatellites for the genetic monitoring of hatchery-produced great scallops.