Abstract: Recently identified genetic markers have enabled us to use marker assisted selection （MAS） in the development of new varieties of pollen-free Cryptomeria japonica（ Japanese cedar, Sugi）; however, numerous technical hurdles persist. In this study, MAS was attempted for quick and easy selection of pollen-free C. japonica from the F2 seedling family after cross pollination of F1 by the single nucleotide polymorphism （SNP） genotyping method using TaqMan probe. F1 trees were resulted from cross pollination between pollen-free C. japonica "Sosyun" and C. japonica plus trees in Ehime prefecture. Consequently, it was possible to distinguish not only the male sterile tree but also heterozygous tree by using the TaqMan probe and primer newly developed from known SNPs. Compared with the SNaPshot SNP genotyping method, this method has significantly lesser number of processing steps and is also time and cost efficient. This method is very useful for MAS of pollen-free C. japonica and is expected to accelerate the development of new varieties in the future.