This study aims to identify and quantify the nitrifying bacterial community with the use of fluorescence in situ hybridization (FISH) technique in a pilot-scale membrane bioreactor achieving efficient biological nitro-en removal from municipal wastewaters. Quantification results revealed that the dominant bacterial phylum and filamentous morphotypes in the bacterial community was high G+C grampositive bacteria. Their relative abundance was 43.2 +/- 4.4 % of the bacterial community. The relative abundance of ammonia-oxidizing microorganisms in the Nitrosomonas cluster, halophilic and halotolerant members of Nitrosomonas, ammonia-oxidizing members of Nitrosospira cluster, and nitrite-oxidizing Nitrobacter spp. were 2.3 +/- 0.18 %, 4.46 +/- 0.83 %, 3.58 +/- 0.18 %, and 2.53 +/- 0.2 % of the total bacterial community, respectively. Nitrifying bacteria were dominated by the members of the genus Nitrosomonas. The relative abundance of total nitrifying bacteria in the sample was 13 % of the total bacterial community. High performance of the membrane bioreactor achieving complete nitrification was considered to be in accordance with the high abundance of nitrifying bacteria found in the system.