Abstract: Rice flower carp is a traditional species in the “Rice-fish co-culture system” in Guangxi Zhuang Autonomous Region, China. Based on partial sequences of D-loop region and Cyt b gene of mitochondrial DNA, the genetic structure of rice flower carp in the Quanzhou (QZ), Rongshui (RS) and Huanjiang (HJ) were studied. A total of nineteen concatenated haplotypes of D-loop and Cyt b sequences were identified in three populations. Haplotype diversity (H_d) and nucleotide diversity (π) were 0.916±0.010 and 0.008±0.004, respectively. Mitochondrial diversities of rice flower carp were characterized by high haplotype diversity and low nucleotide diversity. Among the three populations, the haplotype diversity of HJ was the lowest, but its nucleotide diversity was the highest, which reflects the significant mixture of divergent lineage in HJ population. There was significant genetic differentiation among the three populations (F_st=0.285; P<0.01). Molecular analysis of variance (AMOVA) showed that the genetic variation was mainly within the population (71.54%). Phylogenetic analysis showed that most of the mitochondrial haplotypes in the samples belonged to the haplogroup of C. carpio rubrefusus, and certain frequencies of the mitochondrial haplotypes of C. carpio carpio or C. carpio haematopterus were also detected. Thus, it indicates that the introgressions from cultured common carp breeds may exist. Our study preliminarily revealed the current situation of germplasm resources of rice flower carp in Guangxi, and provided necessary basis for breeding and seedling management of rice flower carp.