The genetic diversity and the phylogenetic relationships of three Cyprinus carpio L. populations were studied by using microsatellite marker technology. It showed that the genetic diversity level of three Cyprinus carpio L. populations was high, population was the highest, WS population was lower,and DP population was the lowest. In order to check the depature of microsatellite loci from HWE, the genotypic frequencies were calculated. Furthermore,32 cases of observed heterozygosity excess(Fis <0) were observed in three populations. The genetic similarity index between WS population and SY population was the highest(0.8320) among the three populations, and their genetic distance was the lowest (0.1680),which indicated that the phylogenetic relationship between these two populations was quite close. On the other hand, the genetic similarity index between WS population and DP population was the Iowest(0.8288),and their genetic distance was the highest(0.1712),which indicated that the phylogenetic relationship between ihese two populations was quite far.