This research assessed the seasonal effects of contrasting tillage and crop rotation systems on soil ammonia oxidizing bacteria (AOB) and archaea (AOA). Four different cropping systems under till and no-till were analyzed in a 30 year-old agricultural field trial. Samples were collected during the 2010 growing season at times corresponding with agronomic events. Nucleic acids were preserved in the field and subsequently analyzed by quantitative real-time polymerase chain reactions (qPCR). Tillage decreased AOB activity and abundance in the plow layer (0-15 cm) immediately after fall moldboard plow events, but observed AOB dynamics at other times suggest tillage had a long-term distribution effect across depth (0-30 cm). AOA abundance was significantly greater in no-till plots at all times indicating tillage had longer-term effects on these communities. Crop rotation had minimal effect on AOB and AOA, but there was a noted yield advantage for corn following wheat, regardless of tillage treatment.