AbstractPseudosciaena polyactis is a commercially important fish species which is widely distributed in the Bohai Sea, the Yellow Sea and the northern part of the East China Sea. Forty-eight individuals of P. polyactis from five sampling areas in the Yellow Sea and the East China Sea were analyzed by random amplified polymorphic DNA (RAPD) markers to determine the genetic variation among and within the stocks. A total of 145 loci were amplified using 20 random primers, of which 132 loci (91.03%) were polymorphic. Genetic diversity quantified by Shannon index varied from 1.50 to 2.44 with an average of 1.93. Partition of genetic variation indicated that 69% was distributed within stocks and 31% among stocks. The average genetic similarity and genetic distance were 0.9139 and 0.0861, respectively. Cluster analysis by UPGMA indicated that these five stocks might be divided into three groups. Results of RAPD analysis suggested extensive genetic diversity exists in this species and the genetic divergence among stocks is relatively high. The UPGMA dendrogram showed that there existed three geographic populations of P. polyactis in the Yellow Sea and the East China Sea, which supports previous conclusions based on morphological and ecological methods.