Takifugu, belonging to Tetraodontidae in Tetraodontiformes, is the typical adaptive radiation species, and there were about twenty Takifugu species along the coast of China. In this study, phylogeny and population genetics of Takifugu species were analyzed based on population scale for the first time. Using mitochondrial genome, we obtained 1, 488 SNPs and 4 INDELs in 124 individuals of 10 Takifugu species. The phylogeny and population genetics analysis showed that T. poechilonotus and T. alboplumbeus could be synonymous, and the sister group of these two species was located at the base of phylogeny tree. Besides, we found that the relationships between T. rubripes and T. fasciatus, T. flavidus and T. bimaculatus were close. In addition, we detected 4 T. bimaculatus individuals which possibly were the hybrid progenies with T. flavidus, and 2 hybrid suspect T. oblongus individuals. For genetic diversity, we found that T. alboplumbeus has the lowest diversity. Moreover, we identified 595 species Species-specific SNPs in 10 Takifugu species. The Ka/Ks analysis showed that cox1 had the lowest Ka/Ks, and the Ka/Ks of nd6 was 1.19, which indicated that nd6 possibly has undergone positive selection. Besides, the ATP synthetase might be under selection in the process of adapting to fresh water of T. ocalletus and T. fasciatus. This study showed that the phylogenetic relationship of Takifugu was complicated. Although the natural hybridization between species was common in the wild, this study can provide reliable molecular markers for the rapid identification of Takifugu species, and provide a solid foundation for the study of the Takifugu phylogeny in the future.