In this study,all the dominant anammox bacteria were distributed over two genera,Candidatus Brocadia and Kuenenia,in four anammox reactors. It was shown that sludge morphology played an important role in the bacterial community structure of anammox bacteria. More than 36 percents of anammox bacteria in granular sludge and biofilm belonged to Candidatus Brocadia,while in flocculent sludge the domninant anammmox bacteria was Candidatus Kuenenia. Anammox bacteria in different sludge morphologies would migrate in the same reactor,but the dominant species remained.