Mitochondrial DNA(mtDNA) of Takifugu fasciatus is prepared as templates from the liver tissue.Sev-eral mitochondrial genes,such as 12S rRNA and its connected tRNA genes are amplified by PCR with a pair of specific primers,which is designed based on Takifugu rubripes from Genbank.The specific PCR product are then cloned and sequenced.The total sequence has been submitted to GenBank.The 12S rRNA mtDNA of T.fasciatus is proved to have good homology with 6 species of fish which were selected from the NCBI and their sequences are recorded in the GenBank.The Cyprinus carpio is designated as outgroup.The phylogenetic trees based on the homology of the mitochondrial 12S rRNA showed that the phylogenetic relationships of T.fasciatus with other 5 kinds of fish are consistent with their morphological taxonomy.