Molecular techniques are growing in popularity to study ammonia-oxidizing bacteria (AOB) to avoid the biases of culturing techniques. DNA was extracted from soil that received dairy waste compost (DC), liquid dairy waste (LW) and ammonium sulfate (AS) at approximately 100 and 200 kg available N ha-1 for six years. Real-time PCR was employed to quantify the number of AOB by targeting the gene encoding ammonia monooxygenase, amoA. Clone libraries and the variation in length of the intergenic region between amoC and amoA were used to profile the changes in AOB community structure due to treatment. Changes in function of AOB were studied by measuring nitrification potential and gross nitrification rates. The mean number of AOB in soils that received the control, AS200, DC200, and LW200 treatments was 6.1*105, 7.9*106, 2.0*106 , and 1.7*106 cell g-1 soil respectively. Profiles of the amoC-amoA intergenic region indicated that both Nitrosospira and Nitrosomonas type AOB were present in all soils. Similarity indices showed that the band patterns associated with AS and LW treatments were more similar to each other than those associated with the DC treatments, suggesting differences in AOB community composition. Clone libraries indicated that Nitrosospira similar to Nitrosospira multiformis were numerous in all soils examined while Nitrosomonas-like sequences were detected only in the LW200 treated soils. Gross nitrification rates were higher in plots receiving the DC treatments (averaging 10 mg N kg-1 soil day-1 for high rate treatment) while the rate of application was more important in determining nitrification potentials. Relatively simple and quick PCR techniques were effectively used to quantify and profile AOB in an agricultural soil that received repeated application of dairy waste.