Although several different U.S. hatchery stocks of the Asian Suminoe oyster Crassostrea ariakensis were used in laboratory and field trials assessing performance, and in comparative studies with the native oyster Crassostrea virginica, the genetic composition of these hatchery stocks has not yet been examined comprehensively. Using eight microsatellite markers we investigated the genetic variability among five hatchery stocks and compared the genetic makeup of these stocks with 8 wild populations from Asia. Results showed significant genetic differentiation among the 5 hatchery stocks that was 6-fold larger than that observed among wild populations. A significant reduction in genetic diversity was observed in hatchery stocks compared with wild source populations, indicating a genetic bottleneck. Two long-established stocks showed significant decreases in both allelic diversity and heterozygosity compared with the wild Japanese source population, whereas three recently established stocks showed less severe reductions in allelic diversity and a nonsignificant change in levels of heterozygosity compared with their source Chinese populations. These microsatellite markers also proved useful for assignment of hatchery individuals back to their source stocks with a high degree of confidence. Although assignment of wild individuals back to their population of origin proved less reliable, approximately 70% of wild individuals could be assigned either to their source population or to geographically proximal populations. Our results suggest that results obtained from experiments that used hatchery animals of a single C. ariakensis stock for biological and ecological studies should be interpreted cautiously, because they may not always accurately reflect the behavior of wild populations or of other hatchery stocks.