RAPD method was used in analyzing the genetic diversity of two stocks of farmed mandarin fish. Forty random primers were used for the analysis of nuclear DNA polymorphism of two stocks. The results showed that twenty-two primers were effective with 289 bands were obtained by the experiment. Among them, 155 bands were acquired from Guangdong stock, while 134 bands from Hunan stock. Two stocks shared 122 bands. According to the pattern, the average inter-stock genetic distance of Guangdong stock is 0.063 3, while Hunan stock 0.062 9. The intra-stock genetic distance between two stocks is 0.129 9. Values of Shannon diversity of Guangdong stock and Hunan stock were 0.069 0 and 0.072 3 respectively. The percentage of polymorphic loci of Guangdong stock is 25.16 %, a little higher than the average percentage of vertebrate (24.7 %). The percentage of polymorphic loci of Hunan stock is 10.15 % with 14.55 % lower than Guangdong stock and vertebrate. These results suggest that diversity of two stocks is not good. As a result，it implied that effective husbandry and management measures must be taken to avoid reduction of genetic diversity so as to enable the sustainable development of the mariculture.