Seven oligonucleotides decamer primers of the 20 arbitrarily chosen primers were used on the basis of the number of the polymorphisms generated in oyster (Crassostrea gigas) from Buan and Geojedo. Engaged to amplify genomic DNA isolated from the muscle of individual oysters, the random primers OPA-08, -09, -16, -17, -20, OPB-03 and -07 generated common, polymorphic and specific bands. The selected 7 primers generated the total of 481 distinguishable fragments in the oyster population from Buan and 264 in the population from Geojedo. DNA fragments ranged from 50 to 1,600 base pairs (bp). The primer produced the highest number of fragments total 92 among primers used, with an average of 8.4. The average bandsharing value (BS value) within the oyster population from Buan was 0.639 ± 0.013 and Geojedo was 0.537 ± 0.017. The average bandsharing value between two oyster populations was 0.282 ± 0.008, ranged from 0.116 to 0.494. Among individuals, bandsharing values of individuals within the oyster population of Buan were higher than the individuals from Geojedo. The oyster population of Buan was more polymorphic than the population of Geojedo. The difference between two oyster populations was statistically significant. PCR results showed that the oyster population of Buan in the West Sea was genetically more distant than the oyster population of Geojedo in the South Sea. The hierarchial dendrogram obtained with four primers classified them as three genetic clusters: cluster 1 (Case No. 01, 02 and 03), cluster 2 (Case No. 04, 05, 06, 07, 08, 09, 10 and 11) and cluster 3 (Case No. 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 and 22). The genetic distance between two geographic populations ranged from 0.039 to 0.284. The longest genetic distance that displays significant molecular difference was between individual No. 5 and No. 15 (0.284) between two populations. RAPDPCR analysis has revealed the significant genetic distance between two oyster population pairs.