The Community Structure and abundance of ammonia-oxidizing bacteria (AOB) in membrane bioreactors (MBRs) constructed to treat different types of wastewater were analyzed by PCR-DGGE, cloning of 16S rRNA fragments and quantitative real-time PCR techniques. DGGE analysis revealed that the diversity of the ammonia-oxidizing bacterial communities was similar among the four reactors. Additionally, variation in influents had no significant effect on the distribution of the AOB communities. Sequencing analysis of screened clones revealed a wide variety of nitrifying organisms and denitrifying bacteria, which Suggests that there may be Multiple modes of nitrification and denitrification in MBRs. Real-time PCR revealed that the AOB comprised less than 0.1% of the total bacteria in all MBRs. The free ammonia content of the influent was well correlated with the AOB cell numbers. Taken together, these data suggest that higher NH4+-N content favors the growth of ammonia oxidizers in MBRs. Crown Copyright (C) 2009 Published by Elsevier Ltd. All rights reserved.