In order to estimate genetic differences and variability among and within cultured stocks of the masu salmon complex, restricition-fragment length polymorphisms (RFLP_s) of mitochondrial DNA (mtDNA) were performed for three masu salmon (Oncorhynchus masou masou) stocks and one amago salmon (O. m. macrostomus) stock. Based on our RFLP analysis using six 6-base recognized restriction endonucleases (BamHI, BglII, EcoRV, Hincll, HindIII, and XbaI), we concluded that: 1) the total size of mtDNA was about 17.3±0.5Kbp, 2) thirteen mtDNA haplo-types were observed among 59 individuals of the 4 stocks, 3) major haplotypes were different from each other and stock-specific haplotypes were observed in three out of four stocks, 4) the nucleotide diversity within the non-selected stocks ranged from 0.00170 to 0.00253, while no variation was observed in selected Amago-parr stock. The results suggest that the Amago-parr stock consists of only one maternal line while the other stocks consist of several maternal lines.