DNA polymorphism of thirty individuals of each of the three migrating reproductive populations of Gymnocypris przewalskii (Kessler) in the Qinghai Lake was analyzed by random amplified polymorphic DNA (RAPD) , which were Heimahe population (HM) , Buhahe population (BH) and Shaliuhe population (SL) . A total of 85 loci , including 68 polymorphic ones , were detected from the three populations by using 13 primers. The average percentage of polymorphic loci to total DNA of the three populations was 80. 0 %. The results of data analysis showed that the populations had on average the Nei’s value of 0. 3395 for gene diversity and the Shannon’s information index of 0. 4861 , there existing a relatively abundant genetic diversity. The average genetic distance among the three populations was 0. 0788. The gene differentiation coefficient ( Gst) of 0. 1070 indicated that there was genetic differentiation of a certain degree among the three populations. Clustering analysis by UPGMA method showed that HM and BH were clustered with priority, indicating that the gene flow of both populations was more frequent than that between either and SL.