Abstract: The Takifugu fasciatus mitochondrial cytochrome Oxidase I gene (COI) and its connected tRNA genes were sequenced by PCR. The open reading frame of COI gene contains 1546bp nucleotides, encoding a putative protein 515 amimo acids. The pattern of codon usage of the COI gene is less biased of A+T. The COI gene of Takifugu fasciatus was proved to have good homology with the other 13 species of fish recorded in the GenBank and it has 97.6% homology with Takifugu rubripes. The phylogenetic trees show that the relationships based on the homology is consistent with the morphological taxonomic results. Assumed secondary structures of tRNA genes suggest that they have the classical cloverleaf structures.