This study was conducted to identify bacteria responsible for the elimination of sludge in an innovative gravel contact oxidation reactor (GCOR) and a conventional activated sludge reactor (ASR). Fluorescent in situ hybridization revealed that α-, β-, γ- and ε-Proteobacteria and Bacteroidetes were present in both reactors. In the GCOR, γ-Proteobacteria accounted for 13% of the biofilm biomass on the carrier, while α-, ε- and β-Proteobacteria accounted for 12%. However, the predominant bacteria in the pores of the carrier in the GCOR were Bacteroidetes (18%), ε-Proteobacteria (13%), β- and α-Proteobacteria (10%) and γ-Proteobacteria (9%). Conversely, β-Proteobacteria (18%), Bacteroidetes (13%), α- and γ-Proteobacteria (12%) and ε-Proteobacteria (5%) dominated the sediment community of the ASR.