pairs of microsatellite primer were designed to characterize the genetic diversity within wild Cyprinus carpio and two cultivated stains, and the genetic relationship among them. The microsatellite data indicated that the average heterozygosity of three populations is 0.64, 0.40 and 0.38 respectively, demonstrating that the genetic diversity of wild common carp is the highest, and the frigid carp is more diversified than cold tolerant strain of red carp resource. This reveled that the artificial propagation and selective breeding maybe decrease genetic diversity. In this study, one population specific marker 209bp was found, it laid the foundation for further research concentrating on the linkage between the traits and the marker, and for molecular assistant breeding in fish. The genetic distance of three populations was calculated and cluster analysis was also carried out. The phylogeny reconstructed by the microsatellites data conformed to the artificial propagation operation of the cultivated strains.