Genomic DNA samples isolated from geographical purple Washington clam (Saxidomus purpuratus) were obtained from two different regions in Korean Peninsula: Gunsan (Gunsan population; GSP), and Haeju (Haeju population; HJP), a collection area in the vicinity of the West Sea. The seven arbitrarily primers, OPA-07, OPA-09, OPA-18, OPA-20, OPC-03, OPC-06 and OPC-09 were shown to generate the total loci, loci observed per primer, shared loci by each population, specific, and polymorphic loci which could be clearly scored. We also generated the unique shared loci to each population and shared loci by the two populations in purple Washington clam. The size of the DNA fragments also varied wildly, from 50 to 2,400 bp. Here, 304 total loci were identified in the GSP purple Washington clam population, and 282 in the HJP: 91 polymorphic loci (29.9%) in the GSP and 47 (16.7) in the HJP. 198 shared loci, with an average of 28.3 per primer, were observed in the GSP population. The decamer primer OPA-07 generated the shared loci by the two populations, approximately 1,000 bp, between the two Saxidomus populations. The oligonucleotide primer OPC-03 also generated the shared loci by the two populations, approximately 500 bp and 1,000 bp, in GSP population from Gunsan and HJP population from Haeju. The other primer, OPC-06 generated the shared loci by two Gomphina populations (approximately 400 bp). The dendrogram, generated by seven reliable primers, indicates three genetic clusters. The dendrogram obtained by the seven primers indicates three genetic clusters: cluster 1 (GUNSAN 01-GUNSAN 02), cluster 2 (GUNSAN 03-GUNSAN 11), and cluster 3 (HAEJU 12-HAEJU 22). The genetic distance between the two geographical populations ranged from 0.043 to 0.506. Especially, the longest genetic distance displaying significant molecular differences, 0.506, was found to exist between individuals GUNSAN no. 11 of Gunsan and HAEJU no. 17 of Haeju.