The hard clam(Meretrix meretrix) is a commercially important shellfish in China. With the rapid development of the aquaculture industry of M. meretrix, the demand for seed cultures has led to the over-exploitation of natural populations, which makes stock enhancement a high priority. Stock enhancement programs that use a small number of breeders for the production of hatchery-reared juveniles to be released to the environment may have negative effects on the genetic diversity of wild populations due to a reduction in the genetic variability of the released stock. In this study, the genetic diversity of seven geographical populations(Sinuiju in North Korea; Dandong, Geligang, and Panshan in Liaoning Province; Dongying in Shandong Province; and Rudong and Qidong in Jiangsu Province) of M. meretrix was assessed using the mitochondrial cytochrome c oxidase subunit I(COI) gene and microsatellite markers. We obtained a total of 142 COI sequences. Each COI sequence was 602 bp in length. These sequences contained 14 variant sites, including 12 transitions and 2 transversions. Twenty-two haplotypes were identified, with 12 haplotypes shared among populations. Population-specific haplotypes were identified in the Sinuiju, Dandong, and Qidong population, respectively. The haplotype diversity was highest in Rudong(h=0.900) and lowest in Dongying(h=0.600). The nucleotide diversity was highest in Dandong(π=0.00350) and lowest in Geligang(π=0.00115). Neutral test(Fu's Fs) and mismatch distribution analysis revealed that the hard clam experienced a population expansion event. Analysis of molecular variance(AMOVA) indicated that 71.64% of the genetic variance was within populations and 28.36% of the variance was among populations, demonstrating significant genetic differentiation among populations(P < 0.05). A total of 54 alleles were amplified from 280 individuals by using 7 microsatellite markers, with an average of 7.7 alleles per locus. The mean observed heterozygosity(H_o) and expected heterozygosity(H_e) was 0.387 and 0.7996, respectively. Compared with other populations, genetic diversity in the Jiangsu population was highest, but the difference was not significant(Kruskal-Wallis test, P > 0.05). Among the 49 population-locus combinations(7 populations×7 loci), 18 cases deviated from the Hardy-Weinberg equilibrium(P < 0.05), indicating heterozygote deficiencies. The neighbor-joining tree showed that the haplotypes were not clustered according to geographical location, but some haplotypes from the same or neighboring locations grouped together(e.g. Rudong and Qidong showing geographical clustering). The unweighted pair group with arithmetic mean(UPGMA) phylogenetic tree showed that the Dandong population was grouped with the Jiangsu population, suggesting that the introduced Jiangsu clam seed has contaminated the genetic background of the Dandong population. These results highlight the need to monitor the genetic effects of releasing large numbers of juveniles.