The 5-stage biological nutrient removal (BNR) process with step feed system showed a very stable organic carbon and nutrient removal efficiency ($87\%;COD,;79\%;nitrogen,;and;87\%$ phosphorus) for an operation period of 2 years. In each stage at the pilot plant, microbial communities, which are important in removing nitrogen and phosphorus, were investigated using fluorescence in-situ hybridization (FISH) and 165 rDNA characterization. All tanks of 5-stage sludge had a similar composition of bacterial communities. The totat cell numbers of each reactor were found to be around $2.36-2.83{ imes}10^9$ cells/ml. About $56.5-62.0\%$ of total 4,6-diamidino-2-phenylindol (DAPI) cells were hybridized to the bacterial-specific probe EUB388. Members of ${eta}$-proteobacteria were the most abundant proteobacterial group, accounting for up to $20.6-26.7\%$. The high G+C Gram-positive bacterial group and Cytophaga-Flexibacter cluster counts were also found to be relatively high. The beta subclass proteobacteria did not accumulate a large amount of polyphosphate. The proportion of phosphorus-accumulating organisms (PAOs) in the total population of the sludge was almost $50\%$ in anoxic-1 tank. The high G+C Gram-positive bacteria and Cytophaga-Flexibacter cluster indicate a key role of denitrifying phosphorus-accumulating organisms (dPAOs). Both groups might be correlated with some other subclass of proteobacteria for enhancing nitrogen and phosphorus removal in this process.