A method for identification of fish species using three different mitochondrial DNA regions, 16S rRNA, cytochrome b and cytochrome c gene fragments, was investigated. The combined use of all three regions enabled reliable species identification in not only raw fish, but also dried, seasoned and boiled fish, products. Furthermore, the method was applicable even to vomitus from a patient involved in a puffer fish poisoning incident. However, further improvement is necessary to discriminate between closely related species such as Takifugu rubripes and T. chinensis, because they showed close similarity in the nucleotide sequences in the three gene fragments analyzed in this study.