An autotrophic denitrification reactor (ADR-1) and a heterotrophic denitrification reactor (HDR-2) were operated to remove nitrate and nitrite in an anoxic environment in raw sewage. The NO3-N removal rate of ADR-1 was shown to range from 52.8% to 78.7%, which was higher than the NO3-N removal rate of HDR-2. Specific denitrification rates (SDNR) of ADR-1 and HDR-2 were 3.0 to 4.0 and 1.1 to 1.2mgNO3- N/gVSS/h, respectively. From results of restriction fragment length polymorphism (RFLP) of the 16S rRNA gene, Aquaspirillum metamorphum, Alcaligenes defragrans, and Azoarcus sp. were beta-Proteobacteria that are affiliated with denitrifying bacteria in the ADR-1. Specifically, Thiobacillus denitrificans was detected as an autotrophic denitrification bacteria. In HDR-2, the beta-Proteobacteria such as Denitrifying- Fe-oxidizing bacteria, Alcaligenes defragrans, Acidovorax sp., Azoarcus denitrificans, and Aquaspirillum metamorphum were the main bacteria related to denitrifying bacteria. The beta-and alpha-Proteobacteria were the important bacterial groups in ADR-1, whereas the beta-Proteobacteria were the main bacterial group in HDR-2 based on results of fluorescent in situ hybridization (FISH). The number of Thiobacillus denitrificans increased in ADR-1 during the operation period but not in HRD-2. Overall, the data presented here demonstrate that many heterotrophic denitrifying bacteria coexisted with autotrophic denitrifying bacteria such as Thiobacillus denitrificans for nitrate removal in ADR-1. On the other hand, only heterotrophic denitrifying bacteria were identified as dominant bacterial groups in HDR-2. Our research may provide a foundation for the complete nitrate removal in raw sewage of low-COD concentration under anoxic condition without any external organic carbon or the requirement of post-treatment.