In the activated sludge process, the share of filamentous bacteria is crucial for proper settlement and high sewage treatment efficiency. Disequilibrium of the microbial community may be a reason for the appearance of bulking episodes. During 19 months (August 2007-February 2009) activated sludge samples were collected and analyzed by physicochemical, microscopic, and molecular methods. Amplified ribosomal DNA restriction analysis was chosen to detect molecular changes between normal and bulking sludge samples, which may be markers, informing about disadvantageous changes in the microbial population. Quantity and length of restriction products were the basis to create dendrograms representing the phylogenetic relationship of activated sludge samples. The most suitable restriction enzymes for finding molecular differences between normal and bulking sludge were MspI and HhaI.