Microsatellite DNAs were used to analyze the variations and structures of three geographic populations of Cirrhina molitorella in Xijinag (XJ), Beijiang (BJ), and Dongjiang (DJ) in the Pearl River Basin as well as one cultured population. The genetic diversity was calculated using microsatellites. This data revealed high genetic variations in both wild and cultured populations of C. molitorella, with average He ranging from 0.7081 to 0.7723. The analysis of molecular variance (amova) showed that only 5.76% of the variance was among populations, whereas 94.24% of the variance was within populations. Exact testing for non‐differentiation showed insignificant differentiation among populations (P > 0.05), but a phylogenetic tree calculated in Phylip produced evidence for some differentiation between wild and cultured populations.