To study spatial variation in natural tree seedling density and the relationship between variation in seedling density and seed dispersal mode at a cleared site, we surveyed natural tree seedlings after the site preparation for planting in a coniferous plantation cleared by a typhoon disturbance in 2004. The site was located near Sikotsuko Lake, Hokkaido, northern Japan. Twenty-five tree seedling species were found and the mean seedling density was 9.8 seedlings/m2. Seedlings of non-animal-dispersed species (7.2 seedlings/m2) were approximately five times more abundant than those of animal-dispersed species (1.4 seedlings/m2), and 87% of all seedlings were current. The seedling density of non-animal-dispersed species (almost all wind-dispersed) decreased with distance from a natural forest; however, this trend did not hold for animal-dispersed species (almost all bird-dispersed). The spatial variation in seedling density was lower in animal-dispersed species than in non-animal-dispersed species. Seed dispersal patterns and the viability duration of buried seeds likely affected the variation in seedling density by seed dispersal mode.