Black sea bream, Acanthopagrus schlegelii, is a commercially important fish in Korea. As a preliminary investigation into the effect of hatchery rearing for stock enhancement, we examined genetic diversity between wild and farmed black sea bream populations from Jeju using six microsatellite markers. High levels of polymorphism were observed between the two populations. A total of 87 different alleles were found at the loci, with some alleles being unique. Allelic variability ranged from 8 to 22 in the wild population and from 7 to 17 in the farmed one. Average observed and expected heterozygosities were estimated at 0.87 and 0.88 in the wild sample. The corresponding estimates were 0.83 and 0.86 in the farmed sample. Although a considerable loss of rare alleles was observed in the farmed sample, no statistically significant reductions were found in heterozygosity or allelic diversity in the farmed sample, compared with the wild one. Significant genetic heterogeneity was found between the wild and farmed populations. These results suggest that more intensive breeding practices for stock enhancement may have resulted in a further decrease of genetic diversity. Thus, it is necessary to monitor genetic variation in bloodstock, progeny, and target populations and control inbreeding in a commercial breeding program for conservation. This information may be useful for fisheries management and the aquaculture industry.