More than two decades ago Kumamoto oyster Crasosstrea sikamea was crossed with pacific oyster Crassostrea gigas in a commercial hatchery in the hope to produce a oyster with good qualities of both species. Despite of the continuous efforts to select the broodstock oyster by morphology hatchery produced seed of Kumamoto oyster has been reported to grow up resembling Pacific Oyster. The technology to distinguish genetic differences between Kumamoto and Pacific oysters was developed at Dr. Hedgecock’s laboratory at Bodega Bay, California. In this study, the molecular markers were used to select pure Kumamoto oysters for future commercial broodstock. Audactor muscles of the oysters were relaxed by holding the oysters in a magnesium chloride solution in order to remove a small peice of gill tissue for DNA analysis. Each oyster and sample of gill tissue were numbered accordingly and oysters placed into running sea water for recovery. According to the results of the DNA analysis, true Kumamoto oysters were conditioned for spawning, spawned, mated pair-wise by selecting individuals from different origin in the hope of genetic diversity, larvae was reared through metamorphasis, set and delivered to commercial growing grounds for future commercial broodstock oysters. A total of 810 oysters were analyzed and 730 were identified as true Kumamoto oysters which have been sent to commercial hatcheries for pure Kumamoto oyster broodstock.