The degradation of freshwater quality induced by cyanobacterial blooms is a major global environmental concern. Microbially driven nitrogen removal could alleviate eutrophication to some degree in freshwater ecosystems. However, the response of anaerobic ammonium oxidizing (anammox) bacterial communities to cyanobacterial blooms remains poorly understood, especially in reservoir ecosystems. Here we compared the dynamics of anammox bacterial communities during and after a cyanobacterial bloom in a subtropical reservoir. Our data showed that a cyanobacterial bloom triggered a significant increase in bottom anammox bacterial abundance. During the bloom period, anammox bacterial abundance in bottom waters was 9-fold and 52-fold higher compared with non-bloom stratification and mixing periods, respectively. The community composition of anammox bacteria in surface waters changed substantially accompanied by the disappearance of the cyanobacterial bloom, and a shift of dominance from unidentified anammox genera to Ca. Brocadia was observed. Although Ca. Brocadia was always predominant in both middle and bottom waters, the non-bloom period had more unique taxa than the bloom period. Cyanobacterial bloom-related changes in environmental conditions (e.g. NH4-N and total organic carbon) and water stratification together influenced the distribution and dynamics of anammox bacteria. Altogether, our study lays the basis for a better understanding of the breakdown of cyanobacterial blooms in a stratified reservoir.