Abstract: In this study we employed ten microsatellite markers to analyze the genetic diversity of five silver carp populations including Zigui, Wushan, Yunyang, Zhongxian and Mudong in the Three Gorges Reservoir of the Yangtze River. A total of 161 different alleles were detected, and 84 of them were common in all 5 populations. The number of alleles per locus ranged from 7 to 29. In the five populations, the average values of observed and expected heterozygosity ranged from 0.784 to 0.846 and 0.828 to 0.847 respectively, and the mean PIC was 0.797 to 0.817. The Fst values were between-0.001 and 0.009, which indicated that the genetic differentiation was not significant. Chi-square test was used to analyze the genotypes based on the Hardy-Weinberg equilibrium, and the P value indicated that some loci in three populations deviated from the HWE. The bottleneck analysis revealed that the silver carp populations from the Three Gorges Reservoir of the Yangtze River might have undergone a recent genetic bottleneck. The genetic similarity coefficient of the five populations was between 0.891 and 0.950, and the genetic distance of the populations was between 0.050 and 0.115. We also constructed the phylogenetic tree of the five silver carp populations based on Nei's standard genetic distance, and the results showed that genetic distances between the populations were consistent with their geographical distances. The Bayesian analysis also suggested that the silver carp samples from the 5 locations of the Three Gorges Reservoir could be characterized as a single population. Although we did not observe the genetic differentiation, silver carp populations in the Three Gorges Reservoir displayed high genetic diversity. Our study provided valuable information on the genetic resources of silver carps in the Three Gorges Reservoir and in the upstream of the Yangtze River, which should help develop appropriate policies on the conservation and utilization of silver carps.