The dominant nitrifying bacterial communities and nitrification performance of two biological nutrient removal plants were evaluated. Fluorescent in situ hybridization was used to detect and quantify the dominant nitrifying bacteria and polymerase chain reaction; cloning and sequence analysis of 16S rRNA genes was done for phylogenetic analysis. Fluorescent in situ hybridization-confocal scanning laser microscopy studies revealed the presence and dominance of Nitrosomonas-related ammonia-oxidizing bacteria (AOB) and Nitrobacter-related nitrite-oxidizing bacteria (NOB); however, a significant variation in AOB/NOB ratios was recorded. The plant with an overall higher AOB/NOB ratio (> or = 1.0) and dissolved oxygen concentration (1.8 to 2.5 mg/L) showed a higher nitrification rate. This study has also shown the co-existence and variation in phylogenetically diverse Nitrosomonas-related AOB and Nitrobacter-related NOB at these two plants. These dissimilar, distinct distribution patterns of nitrifying communities could be attributed to wastewater characteristics and the process configuration, which, in turn, would have also affected the nitrification performance of the systems.