Abstract: In order to understand the genetic diversity and distribution of silver carp (Hypophthalmichthys molitrix) in the lower reaches of the Yangtze River, we used simple sequence repeats (SSR) combining with capillary electrophoresis to analyze 327 DNA samples of silver carp from eight wild populations in Yangtze River sections (Hukou, Anqing, Wuhu, Dangtu, Zhenjiang, Jingjiang, Zhangjiagang and Changshu sections) from 2017 to 2019, so as to investigate their genetic diversity, genetic differentiation and genetic structure. The results show that the genetic diversity of the eight populations was high. However, heterozygotes were not enough in the populations. The number of alleles ranged from 6.00 to 12.3, while the number of effective alleles ranged from 3.94 to 6.10. The observed heterozygosity and expected heterozygosity ranged from 0.617 to 0.719 and from 0.658 to 0.774, respectively. The unbiased expected heterozygosity ranged from 0.671 to 0.782. The Shannon's information index ranged from 1.38 to 1.86, and the inbreeding coefficient ranged from 0.001 to 0.174. The genetic differentiation analysis shows that the F_st value ranged from 0.006 to 0.068, while the gene flow ranged from 3.41 to 41.9. The genetic distance ranged from 0.001 to 0.106. Hukou population showed a moderate degree of genetic difference with the other populations, while the genetic differences among the other populations were small. Analysis of molecular variance shows that the variation mainly was within the population (97.6%). Genetic structure analysis shows that Hukou population had different gene pool from the other populations. The river-lake connectivity may be of positive significance for silver carp to show unique genetic differentiation characteristics in Hukou section of the Yangtze River. Therefore, whether the formation of this population differentiation is caused by the spatial isolation of geographical distance or the physiological barrier of habitat difference needs to be further studied.