Trionyx sinensis is regarded as a very important fishery animals with high economic value.However,the germplasm resources of Trionyx sinensis are exposed to admixture and degeneration due to the booming industry. The investigation of genetic diversity of Trionyx sinensis is beneficial to protect the germplasm resources.In the present study,the variation and genetic diversity of mtDNA D-loop region partial sequences in three geographical populations of Trionyx sinensis were analyzed by PCR combined with DNA sequencing and SSCP techniques.The average contents of A T(65.4%)were higher than that of G C (34.6%).A total of 7 variable sites(about 5.7% of the total nucleotides in the sequence)were detected in 25 individuals,and the value of si/sv was 2.76.The nucleotide diversity(π)of the 25 individuals was 0.019 95, and the average number of nucleotide differences(K) of them was 2.453.The 25 individuals belonged to 6 haplotypes according to the determined sequences.The haplotype diversity (H_d)was 0.707,and the average genetic distance(P) among the haplotypes of the species was 0.027.The analysis of phylogenetic tree with the method of UPGMA showed that the 6 haplotypes were clustered into three groups.Our data indicated that the variation and genetic diversity were high in the three populations of T.sinensis, in which the genetic diversity of Japanese population was richer than that of Huanghe and Huangsha population,and the genetic distance between Huangsha population and the other two populations was far.Moreover,we found that two types of electrophoretic patterns could be detected by PCR-SSCP,and all type Ⅱwere Japanese population,suggesting the effective application of PCR-SSCP method in 78 TT-AA transversion mutation sites testing.