In this study, the microbial community for denitrification in the down-flow hanging sponge (DHS) reactor was estimated by batch experiment and microbial community analysis. Sludge retained from the DHS reactor, which conducts single-stage nitrification-denitrification, was collected into a series of vials as seed sludge for the batch experiment. Nitrate, nitrite, and nitrous oxide were added as nitrogen sources for each vial series. Sodium acetate solution was added to each vial series as a carbon source. At the beginning of the batch experiment, nitrous oxide was accumulated from only the nitrite-fed series (NO2 series). Approximately 50% of reduced nitrate was accumulated as nitrite in the nitrate-fed series (NO3 series). After two weeks of cultivation, nitrous oxide began to accumulate in the NO3 series without nitrite accumulation. Nitrous oxide accumulation was not confirmed in the NO3 series after 15 days of cultivation. During the batch experiment, the predominant denitrifying bacteria changed from Alicycliphilus to Thauera in the NO3 series. By contrast, the nitrous oxide producer Propionibacterium and the nitrous oxide reducer Staphylococcus increased in the NO2 series only. Thus, nitrite accumulation was considered to be a key factor for nitrous oxide emission in the DHS reactor. In addition, it was suggested that both nitrifying and denitrifying bacteria contributed to prevention of nitrite accumulation in the DHS reactor.