The effects of volatile fatty acids (VFAs) on nitrogen removal and microbial community structure in nitritation/anammox process were compared within a granular sludge reactor and a moving bed biofilm reactor. Nitrate productions in both systems were lower by 40-68%in comparison with expected nitrate production. Expected sludge production on VFAs was estimated to be 67-77%higher if heterotrophs were the main acetate degraders suggesting that Anammox bacteria used its organotrophic capability and successfully competed with general heterotrophs for organic carbon, which led to a reduced sludge production. FISH measurements showed a population consisting of mainly Anammox and AOB in both reactors and oxygen uptake rate (OUR) tests also confirmed that flocculent biomass consisted of a minor proportion of heterotrophs with a large proportion of AOBs. The dominant Anammox bacterium was Candidatus 鈥?em>Brocadia fulgida鈥?with a minor fraction of Candidatus 鈥?em>Anammoxoglobus propionicus鈥? both known to be capable of oxidizing VFAs.