Abstract: Cultivated and wild populations of mandarinfish (Siniperca chuatsi Basilewsky) were analyzed using 60 random primers by randomly-amplified polymorphic DNA (RAPD) method. The results indicated that the percentage of polymorphic sites, the genetic similarity rate and the genetic distance in wild population and cultivated population of the mandarinfish were 85.75% and 16.39%, 0.8547 and 0.9527, 0.1453 and (0.0473), respectively. The low genetic similarity rate(0.6905) and high genetic distance(0.3095) between two populations indicated that there was a significantly genetic differentiation, suggesting that aquaculture had led to decrease in genetic diversity.