We investigated factors affecting the distribution of naturally regenerated broad-leaved trees in a 140-year-old Cryptomeria japonica plantation. We used path analysis to examine the relationship among microtopography, the biomass of planted trees, and the biomasses of canopy and subcanopy trees of broad-leaved species. The study plot was divided into three topographic types (ridge, slope, and valley), and we discuss how the different topographic types are affected. For all topographic types, the biomass of canopy trees of broad-leaved species decreased with convexity. For slope and valley topographies, the biomass of subcanopy trees of broad-leaved species also decreased with convexity. For ridge topography, the biomass of subcanopy trees of broad-leaved species increased with the biomass of planted trees, and decreased with the biomass of canopy trees of broad-leaved species. These results suggest the effects of microtopography on the biomass of subcanopy trees were much larger than the effects of canopy trees for slope and valley topographies, while the effects of microtopography were smaller for ridge topography.