Studies on the genetic differentiation of two different ecotypes, Oryza sativa japonica and indica, are very important for many aspects including the overcoming sterility barriers in hybrids between two types in cultivared rice. This study was carried out to 1) investigate the genetic variation and differentiation among 34 rice cultivars in two ecotypes using PCR-based markers, RAPD, AFLP and microsatellite-SSR and 2) compare the results of genetic variations derived from each PCR-marker technique. The indica type rices were clustered separately from japonica type rices at the genetic similarity level of 0.75. The genetic similarity among the indica rices was lower than that of japonica type rices. Three cultivars, Fuji269, Sobaegbyeo, Keumobyeo showed very close genetic relatedness since they were indistinguishable in our experiment. Since the utilized PCR-based marker techniques are the most frequently used ones in many areas, the variations detected by each marker were compared with each other. Although differences were not significant in genetic relatedness derived from RAPD, AFLP and microsatellite-SSR separately, AFLP technique was proved to be very effective in detecting genetic variation since it can generate many marker bands in short time.