Species composition and forest structure change with topography. However, mechanisms for topographical vegetation changes are still not well understood, because a topographical gradient is a complex environmental gradient inclusive of many factors. The foot of Mt. Kinabalu is covered with three types of geological substrates, i.e. Quaternary and Tertiary sedimentary rocks and ultrabasic (serpentine) rock. Quaternary and Tertiary sedimentary rocks are different in site age, but controlled in primary minerals. Tertiary sedimentary and ultrabasic rocks are contrasting in primary minerals, but are comparable in age. This setting provides an opportunity to examine the vegetation differentiation along topographical gradients that are contrasting in major-nutrient supply due to the difference in site age and parent rock. We established a total of nine study plots by choosing three topographical units (ridge, middle- and lower-slope) on each substrate in the tropical lower montane forest. Pool size and supply of soil N and P decreased upslope on each substrate, and the magnitude of the reduction from slope to ridge decreased in the order of Quaternary sedimentary > Tertiary sedimentary > ultrabasic rock. Between-substrate difference in soil nutrient condition was greater on the lower-slopes than the ridges. Maximum tree size decreased and stem density increased upslope on each substrate. Detrended con'espondence analysis demonstrated that species composition also changed along topographical gradients on all substrates. Howeven the magnitude of topographical changes in forest structure and species composition varied with substrate and decreased from Quaternary sedimentary > Tertiary sedimentary > ultrabasic rock. The greatest between-substrate difference in vegetation occurred on the lower-slopes. Accordingly, our results suggest that the magnitude of vegetation changes due to topography becomes smaller with decreasing pool size and supply of nutrients.