The abundance and community structure of epilithic diatoms grown on different substrata were investigated in two first-order streams located in a limestone and granite area, north of the Suzuka Mountains in Central Japan. Experiments were conducted as follows: limestone and granite without algae were submerged in their own streambed or another stream station and incubated for seven weeks, while limestone and granite with algae were transferred to another stream station and incubated at the same time. The diatom biomass was consistently high in the lime-stone station experiments compared to those at the granite station. In addition, there was more diatom biomass on granite substrata than on the limestone substrata at both stations. The present results suggested that the difference in water chemistry including the major nutrient concentrations was the limiting factor for algal growth in these two streams; however, when the water chemistry was the same in each stream, the difference in substratum characteristics became the important factor affecting the diatom abundance. The diatom community grown on the transferred substrata with and without algae became similar to those grown on the original substrata in each stream during the incubation period. It was suggested that the effect of the substrata characteristics on the diatom community structure was rather small.