Cryptomeria japonica D. Don (Japanese cedar), an economically important timber species endemic to Japan, is dominant on ridges and upper slopes in cool-temperate natural forests of Kyoto Prefecture. Recruitment of sexual progeny in the area near the Japan Sea is extremely rare, and propagation occurs predominantly through clonal growth by layering. The development pattern that occurs with layering and the resulting complexity of the population structure make it difficult to identify distinct clones, even by excavation. Therefore, we used the randomly amplified polymorphic DNA (RAPD) technique to examine the clonal structure of upper- and lower-slope plots established in two C. japonica populations in Kyoto Prefecture. A total of 263 plants sampled from four plots were analyzed using 10 arbitrarily chosen decamer primers, which produced 50 highly reproducible RAPD bands. There was a different clonal structure in upper- and lower-slope plots. Lower-slope plots were made up of a small number of genets with many ramets, while upper-slope plots were made up of a large number of genets with a few ramets. Clonal diversity measured using PD, Simpson's D, and Fager's E was higher in the upper-slope plots. These results show that natural C. japonica populations maintain relatively high clonal variation, compared with other clonal plant species, and that repeated seedling recruitment occurred more frequently in upper-slope plots than in lower-slope plots.