The clam Meretrix petechialis is a commercially important marine bivalve mollusc, but its population has been greatly reduced because of overexploitation and habitat destruction. In this study, a set of novel expressed sequence tag–derived microsatellite makers were developed and characterized in the clam M. petechialis. The number of alleles at each locus ranged from 4 to 30, with an average of 10.9 alleles per locus. The observed and expected heterozygosities varied from 0.100 to 1.000 and from 0.538 to 0.973, with an average of 0.713 and 0.750, respectively. The polymorphic information content value ranged from 0.423 (Mmt09) to 0.956 (Mmt47), with an average of 0.695. The cross-species amplification transferability of nine microsatellite loci to three closely related species ranged from 29.17% to 100%. These microsatellite loci will be useful for further investigation of the population structure and conversation genetics of this species.