Changes in the fractions of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria in two laboratory-scale reactors were investigated using 16S rRNA probe hybridizations. The reactors were operated in intermittent aeration mode and different aeration cycles to treat anaerobically digested swine wastewater with ammonia concentrations up to 175 mg NH(3)-N/L. High ammonia removals (>98.8%) were achieved even with increased nitrogen loads and lower aeration: non-aeration time ratios of 1h:3h. Nitrosomonas/Nitrosococcus mobilis were the dominant ammonia-oxidizing bacteria in the reactors. Nitrospira-like organisms were the dominant nitrite-oxidizing bacteria during most of the investigation, but were occasionally outcompeted by Nitrobacter. High levels of nitrifiers were measured in the biomass of both reactors, and ammonia-oxidizing bacteria and nitrite-oxidizing bacterial levels adjusted to changing aeration: non-aeration time ratios. Theoretical ammonia-oxidizer fractions, determined by a mathematical model, were comparable to the measured values, although the measured biomass fractions were different at each stage while the theoretical values remained approximately constant. Stable ammonia removals and no nitrite accumulation were observed even when rRNA levels of ammonia oxidizers and nitrite-oxidizers reached a minimum of 7.2% and 8.6% of total rRNA, respectively. Stable nitrogen removal performance at an aeration: non-aeration ratio of 1h:3h suggests the possibility of significant savings in operational costs.