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Two parallel carbon-membrane aerated biofilm reactors were operated at well-defined conditions to investigate the effect of substrate COD/N ratios on the performance and microbial community structure of the bioreactor. Results showed that at substrate COD/N of 5, organic and nitrogen could be eliminated simultaneously, and COD removal degree, nitrification and denitrification efficiency reached 85%, 93% and 92%, respectively. With increasing substrate COD/N ratios, the specific oxygen utilization rates of nitrifying bacteria in biofilm were found to decrease, indicating that nitrifying population became less dominant. At substrate COD/N ratio of 6, excessive heterotrophs inhibited the activity of nitrifying bacteria greatly and thus led to poor nitrification process. With the help of fluorescence in situ hybridization (FISH), Nitrosomonas and Nitrusospira were identified as dominant ammonia-oxidizing bacteria in the biofilm at substrate COD/N of 0, whereas only Nitrosospira were detected in the biofilm at COD/N ratio of 5. Nitrospira were present as dominant nitrite-oxidizing bacteria in our study. Confocal laser scanning microscopy images revealed that at substrate COD/N ratio of 0 nitrifying bacteria existed throughout the biofilm and that at COD/N ratio of 5 they were mainly distributed in the inner layer of biofilm.