The Japanese giant salamander, Andrias japonicus, is known to exhibit very low genetic diversity, but the number of individuals surveyed in a population is limited by now. We investigated partial sequences (673 bp) of mitochondrial cytochrome b gene in 180 specimens of a population from the Inuyama Head Works on the Kiso River, Central Japan, over nine years so as to clarify the degree of genetic diversity. The result again confirmed a tendency of lack of diversity; only one individual differed from the remaining 179 with an uncorrected p-distance of only 1.5%. The individual had the sequence identical with that reported for an individual from San’in District of Western Japan, far from the Kiso River, and is thought to have been introduced artificially. The healthy condition of the salamander population in spite of highly reduced genetic diversities might be due to possible decrease of inbreeding depression, resulting from the past purging effect of ancestral inbreeding wherein deleterious recessive alleles were eliminated from the gene pool.