The objective of this study was to determine the genetic diversity in gilthead seabream broodstocks from two hatcheries on the northern Aegean Coast of Turkey by RAPD-PCR. Forty primers were tested for each broodstock. Twenty-five produced scorable RAPID bands in stock from the Seferihisar hatchery and 28 in stock from the Aliaga hatchery. Nineteen revealed patterns with scorable amplified primers in both broodstocks. Depending on primer, the number of bands varied 3-16, ranging in size from 438 to 2520 base pairs (bp). The average genetic similarity within stocks was 0.466 for the Seferihisar stock and 0.617 for the Aliaga. The average genetic similarity between the two broodstocks was 0.420, lower than the values within the broodstocks, and the genetic distance between the two broodstocks was 0.245.