Thirteen polymorphic microsatellite markers were examined in four different Meretrix lamarckii geographi- cal populations to assess the naturally occurring Meretrix lamarckii resource. The four populations were sampled in Cangnan City, Zhejiang Province; Changle City, Fujian Province; Ningde City, Fujian Province; and Shantou City, Guangdong Province. Sixty-three alleles were found in the 13 microsatellite markers. Allele number per locus was 2–7, and the mean number of alleles was 4.87. Mean effective number of alleles, mean observed and expected heterozygosity, and mean polymorphism information content were 1.927–2.591, 0.437–0.562, 0.446–0.549, and 0.383–0.490, respec- tively. All of these genetic indices indicate medium genetic diversity in the four populations. The Hardy-Weinberg bal- ance test showed that most of the microsatellite sites in the four populations deviated from equilibrium(P<0.05). An unweighted pair group method with arithmetic mean cluster analysis indicated that the Cangnan population clustered with the Ningde population into one clade, and the Changle and Shantou populations were in a second group, which was consistent with their actual geographical locations. The Fst value was 0.230 9, suggesting that the genetic variation in the four M. lamarckii populations was 23.09%, which was high, and that the genetic differentiation level was high.