In this study, four Y-SNPs (M122, P31, M174 and M216) were analyzed in 207 Japanese males (Gunma, Fukui, Kagoshima and Tokushima Prefecture). Eleven Y-STRs, including DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS389, DYS385 and YCAII were also investigated in each prefecture. As a new technique, we used Cycleave PCR method with real-time PCR, which allows detection of Y-SNPs by an easier and faster method. Regarding Y-SNPs, each region in Japan could be almost classified based on two types, the D and O type. We found that the O type was remarkably higher in Kagoshima Prefecture than in other areas. Moreover, the D type was more prevalent than the O type in Gunma Prefecture, which is geographically located at the center of Japan. These findings of geographical differences may be related to the historical background and population movements of Japanese. Y-STRs were analyzed and data from Tokushima Prefecture that we previously reported was included in the analyses. As a result, DYS385 showed the highest gene diversity (GD) value (GD=0.953), while DYS391 showed the lowest GD value (GD=0.288). Haplotype diversity (HD) value of only Y-STRs (Extended haplotype) was estimated at 0.99981, whereas the HD value of Y-SNPs/Y-STRs was 0.9988.