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Microbial community composition in a pilot-scale microfiltration plant for drinking water treatment was investigated using high-throughput pyrosequencing technology. Sequences of 16S rRNA gene fragments were recovered from raw water, membrane tank particulate matter, and membrane biofilm, and used for taxonomic assignments, estimations of diversity, and the identification of potential pathogens. Greater bacterial diversity was observed in each sample (1,133-1,731 operational taxonomic units) than studies using conventional methods, primarily due to the large number (8,164-22,275) of sequences available for analysis and the identification of rare species. Betaproteobacteria predominated in the raw water (61.1%), while Alphaproteobacteria were predominant in the membrane tank particulate matter (42.4%) and membrane biofilm (32.8%). The bacterial community structure clearly differed for each sample at both the genus and species levels, suggesting that different environmental and growth conditions were generated during membrane filtration. Moreover, signatures of potential pathogens including Legionella, Pseudomonas, Aeromonas, and Chromobacterium were identified, and the proportions of Legionella and Chromobacterium were elevated in the membrane tank particulate matter, suggesting a potential threat to drinking water treated by membrane filtration.