In order to determine the effectiveness of DNA fingerprinting as a tool for confirmation of clonal nature and identity, we applied a DNA fingerprinting method to three genetically different groups of ayu Plecoglossus altivelis: clonal diploid, mitotic gynogenetic diploid (mitotic-G2N) and normal diploid. Genomic DNA extracted from blood was digested by Pst I restriction endonuclease and was hybridized with repetitive sequence in bacteriophage M13 DNA labelled with [α-³²P] isotope. DNA fingerprints of P. altivelis were detected over the whole effective fraction range from 0.5-25 Kilobase pairs, and more than 42 fragment patterns were detected. The DNA fingerprints of clonal fish consisted of at least 21 distinguishable bands which showed identical patterns within a clone. Mitotic-G2N consisted of 12-18 bands, and an individual fingerprint of this group hardly shared the bands of the other individuals. A trend of markedly low levels of band sharing in the DNA fingerprint among individuals of mitotic-G2N fish would be useful as a powerful genetic marker for their respective clonal lines. In N-CONT, 9 of the 18-24 distinguishable bands were shared. These results suggest the usefulness of DNA fingerprinting in fisheries genetics as a marker for the assessment of inbreeding rates, and also for the identification of individuals and families.