[Objectives] The Pan’s Box Turtle (Cuora pani) is endemic to China and listed under level-II protection on the “List of Wildlife under Special State Protection”. Due to illegal trade and habitat destruction, its wild population is quite small. The aim of this study was to reveal the genetic diversity and genetic structure of C. pani by using mitochondrial and nuclear gene markers, so as to provide suggestions on population protection and management for C. pani in China. [Methods] In this study, Cyt b, ND4 and R35 genes were sequenced from 14 individuals, including 6 from Guangyuan, Sichuan and 8 of unknown origin. Nucleotide and haplotype diversity and group history dynamics of the samples were determined using DnaSP 5.0 software. The MEGA-X software was used to calculate the variable site, parsimony information site, genetic distance and base content of the sequence, and all haplotypes based on the Kimura 2-parameter model to build maximum likelihood tree. [Results] Results showed that two Cyt b, ND4 and R35 haplotypes were identified in the 14 samples and one new haplotype was identified in each gene (Table 3). The haplotype and nucleotide diversity of each gene marker were Cyt b (haplotype diversity 0.440, nucleotide diversity 0.000 41), ND4 (0.143, 0.000 19) and R35 (0.154, 0.000 63) (Table 4). The average genetic distance (p) of each haplotype was less than 0.01. Phylogenetic analysis based on the three combined gene datasets showed that C. pani and C. aurocapitata were monophyletic clades. Neutral detection and nucleotide mismatch analysis showed that C. pani populations may not have experienced population expansion events in recent history (Fig. 2). [Conclusion] The population of C. pani has low genetic diversity, small intraspecific variation and low ability to cope with environmental changes. Therefore, it is suggested that the basic research and protection of the wild population of C. pani in China should be strengthened, and artificial breeding should be regulated to avoid inbreeding and population recession.