Large waste water treatment plants (WWTP) often operate nitrification in two different process environments: the cold-dilute sewage is treated in the mainstream nitrification/denitrification system, while the high strength ammonia liquors from sludge dewatering are treated in a separate high temperature reactor (SBR). This study investigates transfer from nitrifier biomass into a two-stage WWTP, commonly referred to as bioaugmentation. Besides the quantitation of ammonia oxidising bacteria (AOB), community differences were analysed with two techniques, denaturing gradient gel electrophoresis and real-time PCR melt curve analysis. It was shown that, without bioaugmentation, two distinct AOB communities establish in the mainstream and in the SBR, respectively. A gradual shift of the two AOB communities with increasing pump rates between the systems could be demonstrated. These molecular findings support process engineering experience, that cycling of waste activated sludge improves the ability of AOB to adapt to different process environments.