The three breeds of red carp in Jiangxi Province, namely Cyprinus carpio var. wuyuanensis in Wuyuan County, Cyprinus carpio var. xingguonensis in Xinguo County, and Cyprinus carpio var. wananensis in Wanan County are important cultivation breeds in China. In this paper, random amplified polymorphic DNA (RAPD) was used for molecular biology analysis of genetic diversity among these three red carps for the first time. Forty random primers were used for the analysis of nuclear DNA polymorphism of the three breeds of red carp in Jiangxi Province and wild carp. A clustering analysis was made based on RAPD results with UPGMA and NJ methods in PHYLIP software package (version 3.5) and the phylogenetic trees were constructed. The results show that the intra-breed genetic similarity of Cyprinus carpio var. wuyuanensis is the highest (0.809) and the heterozygosity is the lowest, while the genetic similarity between Cyprinus carpio var. xingguonensis and Cyprinus carpio var. wananensis is the highest (0.745 ), indictating their genetic relationship is closer.