Tropical river waters in South East Asia have been seriously polluted by recent urbanization and industrialization, and microbial ecology of bacteria in tropical rivers must be investigated. In this study, bacterial community structure and their physiological activity in tropical rivers (Kelang River basin, Malaysia) were investigated at a single cell level. Estimates of culturable bacteria on R2A medium accounted for 10 to 30% of DAPI (4',6-diamidino-2-phenylindole)-stained bacteria. The number of bacteria with enzymatic activity, as determined by 6CFDA (6-carboxyfluorescein diacetate), was 10 to 30% of the total bacteria. Bacterial community structures in tropical water samples were analyzed by rRNA-targeted in situ hybridization with HNPP (2-hydroxy-3-naphthoic acid-2'-phenylanilide phosphate) and the direct viable count approach. Forty to 55% of total cells could be detected with EUB338 probe. The bacterial community structure was dominated by the Acinetobacter group in any sample, accounting for 20 to 35% of total cells. Baterial activity and dominant genera were different from those in temperate river samples.