Xenocypris davidi is one of the most economically important freshwater fish in China. In recent decades, owing to the construction of dams, overfishing, habitat degradation, pollution of water, and other human disturbances, the number and biomass of X. davidi local populations declined sharply. On the other hand, X. davidi can effectively restrain the aggravation of eutrophication and control the abnormal proliferation of algae. To restore fishery resources of X. davidi and improve water quality, restocking enhancement activities of X. davidi have been conducted in natural waters since the 1980s. It is urgent to carry out the evaluation of the effect of restocking enhancement of X. davidi, as well as the potential genetic risk assessment of breeding population to wild population of X. davidi under large-scale proliferation and release. However, there has been few report on the effect of restocking enhancement of X. davidi. In order to assess the effect of restocking enhancement of X. davidi and provide guidance and suggestions for the breeding and releasing of X. davidi in Qiantang River, the potential genetic risks of X. davidi in the upper reaches of Qiantang River were evaluated by using 11 polymorphic microsatellite loci. We collected 33 breeding parents and 105 recaptured individuals. Microsatellite DNA molecular marker technology was used. The number of mean alleles (N_a), the mean observed heterozygosity (H_o) , mean expected heterozygosity (H_e) and mean polymorphic information content (PIC) were 8.64, 0.708, 0.739 and 0.703, respectively. It was proved that 11 pairs of microsatellite primers as an effective tool for parentage identification. The combined non-exclusion probability (CEP) of 11 loci was 99.999 980 % by Cervus software. Five individuals were confirmed to be released. The return capture rate of the offspring is 4.76%. The comparative analysis of genetic diversity between the cultured and wild populations of X. davidi showed that the two populations had high genetic diversity, and the genetic parameters of population differed little, indicating that their genetic diversity levels were close; AMOVA analysis showed that genetic variation mainly came from within the population (95.92%), the genetic differentiation coefficient F_ST is 0.053 59, and the gene exchange value (N_m) was 4.42. The results showed that it was a low degree of differentiation and gene communication was barrier-free. So our study suggested that the stock enhancement of X. davidi in Qiantang River had produced a good resource recovery effect, and there was no potential genetic risk caused by the release. In the following studies, on the basis of making full use of microsatellite genotype data, we should strengthen the long-term and continuous tracking of the release population and the field population, so as to provide basic support for the scientific evaluation of the stock enhancement and the conservation of seed resources of X. davidi.