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A total of 159 diatom taxa, mostly pennates, under 35 genera, were encountered on the submersed surface of standing dead trees in Lake Kenyir, Malaysia, during one year of sampling in 1995. Their station wise distribution was 101 taxa at the Dam side (site 1) and 145 taxa at the Petang River (site 2), showing 50% more taxa at the latter station. The spatial variability of diatoms is corroborated by the value of the Jaccard similarity index which was found to be 0.48 between the two stations. The monthly species richness ranged from 22 (November) to 60 (September) at the Dam side, whereas it was 32 (January) to 82 (September) at Petang River. The species diversity ranged from 2.87 to 3.70 and showed a positive correlation with species richness. The pattern in frequency of occurrence of the diatom community was similar at both sites; 35% of the total taxa occurred only once a year in the samples; 31% of the taxa occurred 2–4 times. 15% taxa occurred 5–8 times, and the last 20% occurred 9–12 times in a year. The results of Principal Component Analysis showed that the first and second components comprised 59.4% variability in the data. A general pattern in diatom assemblages can be categorised into four groups along pH gradients. These are group 1: alkalibiont taxa, group 2: heterogeneous mixture of alkaliphilous, circumneutral taxa, group 3: acidobiontic taxa, and group 4: acidophilous taxa. This study showed that the diatom species pool of Lake Kenyir is very rich, like that expected in a tropical waterbody, and the frequency of occurrence of diatom taxa may be related to the niche availability which requires further investigation. Moreover, the spatial variability of diatom communities within the lake is conspicuous, which is probably linked with habitat heterogeneity: Dam side is the main basin of the lake with open deep pelagic zone, and Petang River is a small shallow flowing stream bed comprised of cobbles and boulders.