Aims: To investigate whether two different wastewater treatment plants ( WWTPs) - treating the same pharmaceutical influent - select for a different bacterial and/ or ammonia oxidizing bacterial ( AOB) community. Methods and Results: Molecular fingerprinting demonstrated that each WWTP had its own total bacterial and AOB community structure, but Nitrosomonas eutropha and N. europea were dominant in both WWTP A and B. The DNA and RNA analysis of the AOB communities revealed different patterns; so the most abundant species may not necessarily be the most active ones. Nitritation failures, monitored by chemical parameter analysis, were reflected as AOB community shifts and visualized by denaturing gradient gel electrophoresis ( DGGE)- based moving window analysis. Conclusions: This research demonstrated the link between functional performance ( nitritation parameters) and the presence and activity of a specific microbial ecology ( AOB). Clustering and moving window analysis based on DGGE showed to be valuable to monitor community shifts in both WWTPs. Significance and Impact of the Study: This study of specific community shifts together with functional parameter analysis has potential as a tool for relating functional instability ( such as operational failures) to specific-bacterial community shifts.