Ammonia oxidizing bacteria (AOB) play a key role in the availability and retention of N in ecosystems. Much of our knowledge on the biology and ecology of AOB in soils has come from pure-culture studies. Recent advances in molecular ecology have given us the ability to study AOB with a high degree of resolution, in a range of field contexts. We present results of a field study of the population ecology of AOB on an organically managed tomato farm in Central CA. Community composition and population sizes of AOB were studied using Denaturing Gradient Gel Electrophoresis (DGGE), phylogenetic analysis of clones derived from excised DGGE bands, and both Taqmnan and SYBR green based Real-Time PCR chemistries targeting the amoA gene. A diverse community of AOB with a large total population size was present. Increases in the population sizes in response to N addition were observed. However, changes in community structure in response to N and other edaphic factors were not. This suggests stability in the AOB in this soil at the community level, and plasticity at the population level, over the course of a single growing season. The two real-time PCR chemistries employed here yielded similar results, allowing for greater methodological flexibility in the study of AOB from a range of ecosystems. Soils on organic farms receive high inputs of readily available organic matter, and experience frequent disturbance, aeration, and wet-dry cycles, and this may be conducive to high diversity, activity and stability of the populations of ammonia oxidizing bacteria.