Reject water from a municipal wastewater treatment plant was treated using a stirred tank anammox reactor after being treated by a partial nitrification reactor. The results indicated the variations in the influent NO(2)(-)-N to NH(4)(+)-N ratio had a negative effect on reactor performance, especially when the T-N concentrations were high. Influent total organic carbon concentrations greater than 50 mg/L were proven to have a serious effect on the nitrogen removal efficiencies of the anammox reactor. Observations by scanning electron microscope showed that the surface of the anammox granular sludge was covered by some materials, possibly the effluent SS contained in the partial nitrified reject water. Furthermore, the study of the bacterial composition of the anammox granular sludge showed that the anammox bacterium, Planctomycete KSU-1, was dominant, even during the inhibition phase. (C) 2011 Elsevier Ltd. All rights reserved.