In order to assess the ecological and genetic effects of cutting, we compared two portions of Alnus trabeculosa population at Yuda (Iwate Prefecture, Japan): one that has been cut about 30 years ago and one that has remained uncut. These portions were compared in terms of the degree of sprouting, genetic variation and gene distribution using isozyme markers. First, we determined the multilocus genotype (MLG) of all ramets, then sorted them into individuals according to the distribution of the MLGs. The average (+/- SE) of largest distance between ramets in one individual was 2.1 (+/- 0.18) m, which is consistent with the distance (2.0 (+/- 0.20) m) obtained by tracing physical connections between ramets. We found no significant differences in genetic variation between the two portions, but there were significant differences in their degree of sprouting. Furthermore, there were striking differences in gene distribution: the cut portion showed greater clustering of individuals with identical genetic components, which may be due to regeneration in the gaps made by cutting, reflecting the location of the mother trees, and seed and pollen dispersal from them.