This study aimed to assess stock enhancement of the bighead carp ( is a fish of ecological and scientific significance, inhabiting most of Chinese freshwaters. Moreover, it is one of the most released species in the lower reaches of the Changjiang River. The primary focus of stock enhancement was to release juveniles into natural environments and enhance the stocks of interest. However, the genetic quality of large-scale stock fish is difficult to quantify. Consequently, it is essential to examine the genetic quality of the brood stocks in the hatchery, in order to provide a scientific reference for genetic resource management as well as living resources database construction of brood stocks in the lower reaches of the Changjiang River. During our study, the genetic diversity and population structure of 8 populations were studied using SSR markers. A total of 638 individuals from 7 parent populations and 1 candidate parent population were assayed by 10 pairs of SSR primers. Genetic diversity parameters, principal coordinate analysis (PCoA), and analysis of molecular variance (AMOVA) were generated using Cervus 3.0, GenAlEx 6.501 and Arlequin 3.1 software. Structure and CLUMP software were used to analyze the genetic structure of the populations. The results revealed that the genetic diversity was superior despite inbreeding risk within populations. The average number of alleles was 14.83±1.45, expected heterozygosity and observed heterozygosity were 0.82±0.02 and 0.76±0.05, respectively, while Shannon information index was 2.08±0.09, and inbreeding coefficient was 0.08±0.05. The highest level of genetic diversity was in the candidate parent population. Furthermore, the genetic diversity of parent populations was different. According to structure and PCoA, all individuals could be divided into two genetic clusters, which showed that the genetic differentiation among parent populations were not significantly different, in addition the genetic differentiation between parent and candidate parent populations was significantly different. AMOVA analysis showed that 11% of genetic variation was among the populations and 89% of genetic variation was within populations. The genetic differences between candidate parent and the parent of bighead carp suggest the importance for the introduction and protection of natural germplasm. The results from this study further suggest that it is possible to improve hatchery practices and mitigate the negative effects on wild stocks. However, theoretical support and data reference are required for constructing a healthy and sustainable stock enhancement strategy.