Ten polymorphic microsatellite loci were multiplexed to analyze a total of 343 Pacific oysters (Crassostrea gigas) sampled from native (Japan and Korea), naturalized (France and Australia), and cultured (3 Australian programs) populations. Genetic diversity was high within the native and naturalized populations (average allelic richness, 18.7; expected heterozygosity, 0.89), but lower within samples from hatchery populations (allelic richness, 12.3; expected heterozygosity, 0.84). A significant decrease in diversity was found within Australian cultured populations. However, diversity was shown to be similar in samples from a well-managed, family-based selective breeding population and commercial hatchery mass spawning populations. The Bayesian analysis of population structure found no difference between native and naturalized samples, which, together with other results, indicate that the naturalized populations have not changed genetically since their introduction. This suggests that naturalized populations can provide a good source of genetic diversity for breeding programs.