COⅢ and HNF-1α sequences of Chelydra serpentina were obtained by using PCR amplification and sequencing in order to study the phylogenetic relationships of turtles. The homologous sequences of other turtles were downloaded from NCBI, and analyzed together with the sequences of C.serpentina. After alignment, 757 bp consensus sequences of COⅢ and 769 bp consensus sequences of HNF-1α were obtained. A total of 324 variable sites were detected in the COⅢ sequence, accounting for 42.8% of total sequences, and there were 230 parsim informative sites. The average contents of T, C, A and G were 27.5%, 26.6%, 30.8%, and 15.1% respectively, the content of A+T (58.3%) was bigger than that of G+C (41.7%), and the ratio between transition and transversion was 2.62. In the HNF-1α sequences, we detected 112 variable sites, accounting for 14.6% of total sequences, and 67 parsim informative sites were also found here. The average content was found to be 26.1% in T, 23.1% in C, 28.3% in A and 22.6% in G, the content of A+T and G+C were 54.4% and 45.7%, respectively, and the ratio between transition and transversion was 1.42. Interspecific, intergenus and interfamily genetic distances were calculated based on the kimura-2-parameter model, and the phylogenetic trees were constructed using neighbor joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) methods. The results indicated that kimura-2-parameter distances among 4 genus within Bataguridae based on COⅢ sequences ranged from 0.090 to 0.153, with an average of 0.129, the distances among 7 families within Testudines ranged from 0.150 to 0.207, with average value 0.177, and the kimura-2-parameter distances among 11 genus of Emydidae and Bataguridae based on HNF-1α sequences ranged from 0.003 to 0.051, with an average of 0.016, the distance among Chelydridae , Emydidae and Bataguridae were from 0.044 to 0.067 with average value 0.053. According to the genetic distance and phylogenetic trees, Bataguridae is closer to Testudinidae than that of Emydidae to Testudinidae. The data indicate that Emydidae may be redivided into two clades. Chelydridae and Cheloniidae have a close relationship, while Macroclemys temminckii and C.serpentina may be combined into one genus.