Abstract: DNA samples of four populations ( Gh, Gb, S, J) of clam Meretrix meretrix were analyzed using an optimized RAPD system with high reproducibility. Six primers were amplified bands from 20 primers. The results showed that Gb population had 11 specific bands, and the Gh 2 specific bands, which acted as molecular markers of distinguishing the different populations. The J and S populations had no specific bands. The Gb population had polymorphic locus proportion of 33.33% , and the others had the proportion from 61.54% to 62.86%. The Shannon's index of phenotypic diversity (H) of the Gb was 0. 115, and the others from 0. 189 to 0. 200. The results showed that Gh, J, and S populations had high genetic diversity, surely belonging to Meretrix rneretrix, but the Gb low, indicating that the Gb would be a small population, an independent species or subspecies. Whether Gb group belongs to Meretrix lusoria, Meretrix larmarckii, or even a new species of genus Meretrix needs further research.