Nitrifying bacterial community structures of suspended and attached biomasses in a full-scale integrated fixed-film activated sludge process were investigated by analyzing 16S rRNA gene sequences obtained from pyrosequencing. The suspended biomass had a higher number of ammonia-oxidizing bacterial sequences (0.8% of total sequences) than the attached biomass (0.07%), although most of the sequences were within the Nitrosomonas oligotropha lineage in both biomasses. Nitrospira-like nitrite-oxidizing bacterial sequences were retrieved in the suspended biomass (0.06%), not in the attached biomass, whereas the existence of Nitrobacter-like sequences was not evident. The suspended biomass had higher nitrification activity (1.13 mg N/TSS/h) than the attached biomass (0.07 mg N/TSS/h). Overall, the results made it possible to conclude the importance of the suspended biomass, rather than the attached biomass, in nitrification in the wastewater treatment process studied.