Abstract: Random amplif ied polymorphic DNA ( RAPD) technique was applied to assess the genetic variations among inter- and intra-population of three wild stocks( 24 individuals) in Red Sea Bream from Jiaozhou Gulf (Qingdao ) , Taiwan Strait ( Xiamen) and Beibu Gulf ( Hainan) . Under predetermined optimal reaction conditions, amplifications w ith 31 random primers selected from 60 gave 216 reproducible and stable fragments ranging f rom 200 to 2500bp. There were 176 polymorphic fragment s. Based on the RAPD data, the genetic distances of intrapopulat ion for Jiaozhou Gulf , Taiwan Strait and Beibu Gulf wild stocks were 0. 1350, 0. 1056, and 0. 1151, and similarit ies were 0. 8650, 0. 8944, and 0. 8849. The genet ic distances of interpopulation were 0. 1645, 0. 1413, and 0. 1073. The maximum occurred between Jiaozhou Gulf and Beibu Gulf , the minimum did between Taiwan Strait and Beibu Gulf . This showed there were high genet ic diversity among inter- and intrapopulation. With the methods of UPGMA and NJ in MEGA2. 1 on the basis of genetic distances, the results showed the populations of Taiwan Strait and Beibu Gulf assembled one branch first , then did Jiaozhou Gulf. Both results were accordant .