Abstract: The pufferfishes of the genus Takifugu are East Asian fish, mainly distribute along the coastal region in western part of the Sea of Japan and the East China. This genus is attached more and more importance to researchers, for Takifugu rubripes, which isone species in it, has been a new model fish in the post-genomic era. The detailsof the phylogenetic relationships within the genus remain unresolved. In the present paper, mitochondrial D-loop sequences of 11 species of the genus Takifugu were determined and analyzed to test the present phylogenetic hypotheses1 The sequence saturation analysis was inferred from the shape of the trend line, which indicated that the sequence was unsaturated and could be used in the following phylogenetic analysis. After alignment, the sequence compositions and variations were analyzed by using MEGA 3 software. There were 841 sites, amongwhich 395 siteswere variable, and 267 were informative1 There was significant difference in base compositional bias between the ingroup and the outgroup species1 The uncorrected p-distance matrix obtained from the analysisof the alignment of all D-loop sequences showed that the relationships among the different specieswere closely. Neighbor-joining, Maximum Parsimony, Maximum Likelihood and Bayesian methodswere employed for phylogenetics analysis, respectively. Due to the SH test about the phylogeny hypothesis, we chose the Bayesian tree as our best tree in this paper. The Bayesian tree has described a more clearly phylogeny and the analysis also has pointed out the basal species in the genus. The results indicate that the genus form a monophyletic groups, with the sister group consisted by T. oblongus and T. alboplumbeus is the basal group of the genus1 Our results also show some confusion about the taxonomy in the genus, according to the data and combined analysis with the morphological characters, we suppose some species are in fact synonymous in this genus, which suggest that the taxonomy should be clarified based on both molecular and morphological data in the future.