PCRDGGE and realtime PCR technologies were applied to analyze the relationship between operation efficiency and microbial community structure of the Sequence Batch Biofilm Reactor(SBBR) autotrophic nitrogen removal process.The reactor was possessed of a high nitrogen removal efficiency.And the similarity of microbial community structure between active sludge and biofilm samples was 58.3%. The features of DO distributing on active sludge and biofilm made an appropriate condition for different bacteria.Ammonium oxidation bacteria and anammox were the preponderant bacterium in reactor.And their cometabolisms made TN removal rate reach to 90% and 80%,respectively.The reactor worked under a low efficiency with low concentration of biofilm.It is found that there is no much difference between biofilm and active sludge samples on the microbial community structure.The similarity reached to 100% and the variety of dominant bacteria was poor.Nitrite oxidation bacteria (NOB) were not “washed out” during the setup time that NO3- was accumulated in this reactor.TN removal rate was only about 20% to 30%.