Black sea bream have been intensively stocked in Hiroshima Bay since 1982. However, no information regarding the long-term effects resulting from the release of large numbers of juveniles on the wild population has been reported. We investigated the fate of black sea bream juveniles released at the sampling site from 2000 to 2001 using six microsatellite DNA markers. In 2003 and 2004 respectively, 12.5 and 13.5% of captured black sea bream were identified as hatchery reared. Variation in total length by age between the released and native stocks was not statistically significant. Low FST values confirmed high genetic similarity between wild and hatchery stocks. Pedigree reconstruction confirmed a small loss of genetic variability, with a final inbreeding rate for recaptured fish of around 3% per year, rising to 4% when both years were combined. There was high survival of released black sea bream juveniles. Some of these specimens reached maturity and may have hybridized with their wild counterparts, highlighting the need to monitor the genetic effects of releasing large number of juveniles.