Mitochondrial DNA (mtDNA) of masu salmon among eight populations from six rivers around Hokkaido island were examined to clarify their genetic features and population structure. Restriction fragment length polymorphism (RFLP) analysis using 10 restriction endonucleases (Acc I, Ava I, BamH I, Bgl I, Bgl II, EcoR I, Hinc II, Hind III, Pst I, Xba I) revealed considerable variation. We found 20 haplotypes in 180 specimens. Restriction patterns were polymorphic for 7 enzymes examined. Nucleotide divergence among haplotypes ranged from 0.14 to 2.41%. Nucleotide divergence among populations ranged from 0.49 to 0.70%. Dendrogram constructed by UPGMA among 20 haplotypes showed no clustering groups of localities. Nucleotide diversity and nucleon diversity of each locality ranged from 0.0043 to 0.0072, and from 0.7617 to 0.9304, respectively. These results showed masu salmon populations in Hokkaido have a high mtDNA variability. It is important that high genetic variability be highly regarded in stock enhancement of masu salmon.