Anaerobic oxidation of ammonium (anammox) plays an important role in nitrogen (N) loss from agricultural systems. Recently, the rice rhizosphere was demonstrated to be a hotspot for anammox, yet the dynamics of anammox activity and the distribution of anammox bacteria in rhizosphere soil at different phenological stages of rice growth are still unknown. In this study, the activity, diversity and abundance of anammox bacteria in both rhizosphere and bulk soils were investigated over the entire rice growth season. From tillering to ripening stage, significantly higher anammox bacterial abundance was detected in rhizosphere soils compared to bulk soils. The rhizosphere soils also had significantly higher anammox rates at tillering and booting stages (0.71 and 0.32 nmol N g-1 dry soil h-1, respectively) compared to bulk soils. The anammox rate in rhizosphere soil was positively correlated to the concentrations of NOx- (total of nitrate and nitrite) and acetate. The abundance of anammox bacteria was significantly correlated with the concentration of succinate in rhizosphere soils. A total of five anammox genera of ‘Brocadia’, ‘Kuenenia’, ‘Anammoxoglobus’, ‘Jettenia’ and ‘Scalindua’ were detected, with ‘Brocadia’ predominating in all examined samples. The distribution of anammox bacteria in rhizosphere and bulk soils varied with phenological stages. Statistical analysis indicated that C/N ratio, formate, citrate and ammonium were key factors influencing the composition of anammox bacteria. Variations in activity, abundance and distribution of anammox bacteria in rhizosphere were observed over the phenological progression, demonstrating that the root exudates might be influential for the anammox process. This study implies that future efforts in estimating the rate of anammox should consider the temporal variation during plant life cycle.