Environmental condition is a crucial factor shaping the demography and genetic structure of plant populations. However, we still do not understand how important these environmental factors determine the genetic structure. Cryptomeria japonica is an allogamous coniferous species with wind-mediated pollen and seed dispersal systems. Natural forests of the species are distributed under variable environmental conditions, from Aomori Prefecture to Yaku Island in the Japanese Archipelago. In this study, spatial genetic structure of 12 natural forests inC. japonica were analyzed using eight nuclear microsatellite markers. All trees (stem diameter at breast height over 3 cm) were sampled from 12 natural forest plots (about 40m x 40m). Clonal propagation was detected in many of plots and clonal ratio in each plot varied depending on the site environments. These results suggest that clonal propagation is popular in C. japonica natural forest. Patterns of spatial genetic structure without repeated clones showed significant positive autocorrelation (P < 0.05) over short distances. This pattern may reflect limited seedling establishment in gaps.