Nine microsatellites were developed from expressed sequence tags sequences for the great scallop (Pecten maximus), and were tested in three natural populations. These markers displayed low to moderate levels of variability. On average across all populations, the number of alleles per locus ranged from 1.333 to 8.667, and the observed and expected heterozygosities ranged from 0.029 to 0.703 and 0.028 to 0.711, respectively. All loci conformed to Hardy-Weinberg equilibrium, except PmGC20 in one single population. These new loci might be very useful for the genetic monitoring of the possible impact of aquaculture on the genetic diversity of native scallop populations.