Abstract: Gold grass carp is a kind of grass carp (Ctenopharyngodon idellus) that was introduced from abroad in the 1990s. We used 15 microsatellite markers to analyze the genetic structure and genetic diversity of gold grass carp population and four grass carp populations Yuanjiang (YJ), Ningxiang (NX), Honghu (HH) and Xijiang (XJ) from the Yangtze River and the Pearl River of China. The results show that all the 15 microsatellite loci were highly polymorphic, with polymorphism information content (PIC) of 0.763~0.939. The expected heterozygosity (H_E) of gold grass carp population was 0.662, lower than those of the four Chinese grass carp populations (H_E=0.852~0.885). The analysis of genetic differentiation index (F_ST) indicates that the F_ST between gold grass carp population and YJ, NX, HH, XJ populations were 0.157 2, 0.129 5, 0.147 5 and 0.114 4, respectively. Genetic distance analysis shows that the genetic distance between gold grass carp population and XJ population was the shortest (0.476 3), and was the longest with YJ population (0.810 7). The NJ phylogenetic tree based on genetic distance shows that the four Chinese grass carp populations clustered together as one branch, and gold grass carp population as another. The result shows that the genetic diversity of gold grass carp population is lower than that of Chinese grass carp population, with relative distant genetic relationship.