We examined soil quality characteristics of two long-term observation plots, 1.0 and 0.9 ha, in tropical rain forest in the Mt. Gadut area near Padang, West Sumatra, Indonesia, with regards to tree species diversity. We measured detailed soil chemical and physical properties in 30 × 30 m sized subplots from the two plots. The two 1-ha plots are extending about 1.2 km from a ridge of andesite ⁄ limestone origin where one plot is located to another ridge of shale origins where the other plot is located. Our major aim was to determine whether clear relationships between soil edaphic characteristics and tree species diversity would be recognized. More species and a higher population were found in the plot with low fertility. Furthermore, the variation in soil properties was wider in that plot. To characterize the correlation of spatial distribution between tree species diversity and various soil quality factors, we calculated an omega index of Iwao. The results of comparing species number and various soil properties in 30 × 30 m sized subplots were that the concentrations of elements such as extractable Ca, Mg, AI, Si, Mo, Sr, Sand Zn, as well as the total carbon and total nitrogen showed negative omega values, that is, resulted in a negative correlation, in relation to the species numbers. On the other hand, the variations of the majority of soil quality characteristics, except for extractable Ca, Sand Zn, showed a higher positive correlation to the species number. These results suggest that soil heterogeneity could contribute to creating a diverse edaphic niche for supporting tree species diversity in a few ha size of a few km scale in the Mt. Gadut area. However, this heterogeneous edaphic nature is at least partly the result of the extremely diverse nutritional characteristics of the tree species found in this area.