To investigate bacterial community structure and biodiversity of a CANON reactor that was operated stably at room temperature, total DNA was extracted from the biofilm for PCR-DGGE analysis. The results of microbial community analysis showed that the ammonia oxidizing bacteria Nitrosomonas and Nitrosospira, together with the anaerobic ammonia oxidizing bacteria Candidatus Brocadia and Candidatus Kuenenia were detected as the functional bacteria while nitrite-oxidizing bacteria (NOB) was not found in the CANON system, and the biodiversity of AOB was significantly higher than anammox bacteria. Besides, some other bacteria like Shewanella, Pseudomonas, Ignatzschineria, Dechloromonas and some uncultured bacterium related to Clostridia, α-Proteobacteria and Bacillales also existed in the reactor.