To elucidate sapling patch formation and the mode of regeneration occurring in Chamaecyparis pisifera, we investigated stem distribution and clonal structure of this species in an old-growth beech-conifer forest in central Japan. The study was carried out in a 1-ha plot using small and large sapling (d.b.h. <5 cm, 0.5 m ≤ height < 2 m and d.b.h. < 5 cm, height ≥ 2 m, respectively) and adult (d.b.h. ≥5 cm) stems of Chamaecyparis pisifera. The numbers of small and large sapling stems were 677 and 149 in the plot, respectively, and they were strongly aggregated. Adult stems occurred at much lower density (90 stems in the plot) and were weakly clustered. Fifty multilocus genotypes at nine allozyme loci were detected among sampled stems. Small and large sapling stems with identical genotypes showed aggregated distribution, while some neighboring adult stems had the same genotypes. Spatial autocorrelation of alleles in small and large sapling stems revealed a strongly positive association among stems within a distance of 10 m; but a negative association as distance increased. In adult stems, a strongly positive value was found only in the shortest distance class. These results indicate that clonal growth by layering occurred at the sapling stage and contributed to patch formation. Our results also suggest that the clonal growth by layering is ecologically significant throughout the life history of Chamaecyparis pisifera, particularly as an important strategy for the sapling establishment in the early stage of regeneration process.