Abstract: The 6 geographic populations were analyzed by using mtDNA Cyt b gene sequencing technology for exploring the genetic structure and phylogenetic relationship of rice carp Cyprinus carpio Linnaeus in Congjiang and surrounding areas including Rongjiang, Liping, Jinping, Sanjiang, Tongdao and Jinzhou in China. Among the 447 individuals of rice field carp, there were totally 29 Cyt b gene sequence haplotypes being defined. It was revealed by combining with the phylogeny and sequence comparison analysis of carp homologous sequences in NCBI that the rice field carp in Congjiang and neighboring Miao-Dong areas was a large mixed group containing 2 Eurasian pedigrees, 3 carp subspecies and multiple maternal lineage components, dominated by South China carp C. carpio rubrofuscus. At the same time, the group was also mixed with European carp C. carpio carpio and Far East carp C. carpio haematopterus, which indicated that indigenous rice field carp had experienced genetic invasion by domestic and foreign carp breeding varieties. It was revealed by the genetic diversity analysis that the European carp subspecies population was low H_d and low π type and genetic diversity was poor while the two subspecies populations of Far East carp and South China carp showed the characteristics of high H_d and low π. Among the 6 rice field populations of South China carp, except for Jinping in low H_d and low π, the rest were all high H_d and low π with Congjiang’s H_d being the highest and Liping’s π being the highest. It was shown by genetic differentiation and molecular variance (AMOVA) analysis that there was significant genetic differentiation between lineages and subspecies (P<0.001). Moreover, Jinping and Sanjiang had a medium-high level of differentiation with other populations with the rest populations being weak in differentiation. The contribution rate of variation among these groups was 16.69% and the figure was 81.14% within the groups. It was indicated by comprehensive analysis that there was limited genetic flows among rice field carp populations in Congjiang and adjacent areas with different genetic structures within and between populations. The research helped to enrich the genetic background data related to the rice field carp in the area, which was conductive to providing a theoretical basis for the identification and protection of rice field carp germplasm resources in the Miao-Dong ethnic area at the junction of Hunan, Guizhou and Guangxi Provinces.