In this study, the mitochondrial (mt) genome of Cyclemys dentata was firstly obtained; the relationship of 20 turtles was analyzed based on mitochondrial DNA (mtDNA). According to the mtDNA sequence of Cyclemys atripons which had been published in GenBank (No. EF067858), sixteen PCR primers were designed to amplify the mtDNA sequence of the C. dentata (Table 1). These PCR productions were inserted into the pMD-18T cloning vectors respectively, the restructured vectors were sequenced, and these sequencing fragments were spliced by Lasergene 7.0 software. The structure and gene order of C. dentata mtDNA were determined by referring to C. atripons mtDNA, and using tRNAscan-SE 1.21 to predicted tRNAs. Based on 20 turtles’ mtDNA heavy chain protein-coding genes sequences, three phylogenetic trees were constructed by Maximum parsimony (MP), Maximum-likelihood (ML) and Bayesian methods using three programs, respectively. The results indicated that the total length of mtDNA of C. dentata was 16 489 bp (GenBank No. JX455823), similar to other turtles’ mitochondrial genome, it encoded 37 genes, consisting of 13 protein-coding genes, 2 ribosomal RNA genes (12Sr RNA and 16Sr RNA), 22 transfer RNA genes (tRNAs) and a control region (D-loop) (Fig. 1, Table 2). The bases composition of C. dentata mt genome as same as that of C. atripons, its A T content was 61.51%, and A T content of 13 protein-coding genes were from 57.89% to 67.86%, their GC contents were low (Table 3). The average length of 20 turtles’ mt genomes was 16 692.5 bp, including 34.1% A, 27.0% T, 26.0% C and 12.9% G (Table 4). OL sequence was 28 bp in length; it could fold into a hairpin secondary structure which contained a 10 bp arm and an 8-base ring (Fig. 2). The D-Loop of C. dentata mtDNA contained a central domain (CD), two extended termination associated sequences (ETASs) and three conserved sequence blocks (CSBs) (Fig.3). From the Fig. 4, we knew that the MP, ML and Bayesian trees had analogical topologies, seven species of genus Cuora clustered into a branch, six species of genus Mauremys clustered into another branch, the C. dentata clustered together with the C. atripons. The analysis results of three phylogenetic trees supported the existing classification of these turtles.