Abstract: Black carp Mylopharyngodon piceus, the most important freshwater fish in China, is widely distributed in the Yangtze River and along the Yangtze River. This study developed 12 highly polymorphic loci from 25 polymorphic microsatellite markers to analyze genetic diversity and population structure of 4 wild and 1 aquaculture populations in the Yangtze River system. The results showed that the polymorphic information content (PIC) of these 12 loci was between 0.660—0.923, indicating that all 12 loci were highly polymorphic (PIC>0.5). The allele number (N_a) of the 5 populations was between 7.917—11.667 and the effective allele number (N_e) ranged from 4.837 to 6.035. The observed heterozygosity was between 0.713—0.861 and the expected heterozygosity was between 0.749—0.819. The ave-rage polymorphism information content was between 0.711—0.788. These results indicated the high genetic diversity in all 5 populations. The genetic distance between the 4 wild populations was relatively closer. The genetic distance between the cultured population and the 4 wild populations was much larger than that of the 4 wild populations. In the UPGMA phylogenetic tree, the Xiangjiang population and the Shishou population were first gathered together, and then clustered with the Hanjiang and Jiaxing populations, and finally together with the Wujiang culture population. The 12 microsatellite loci can be used for the assessment of germplasm resources and genetic diversity of different populations in black carp.