In order to discriminate between Porphyra tenera Kjellman and P. tenera Kjellman var. tamatsuensis Miura, the partial sequences (670 bp) of mitochondrial DNA related to ATP6 gene were examined for use as a genetic marker. The partial sequences were identical within the three strains examined of P. tenera var. tamatsuensis, but the sequences had a single substitution compared with the three strains examined of P. tenera. The region used in the present study is concluded as an effective marker for discrimination between P. tenera var. tamatsuensis and P. tenera. Moreover, the sequences of two closely related species P. yezoensis Ueda f. narawaensis Miura and P. tenera had differences of 20-21 bases. Thus, this region may also allow discrimination of species within genus Porphyra.