The presence of organic matter (OM) is considered to affect anammox process adversely, while practically wastewaters containing ammonia are not free from OM. In this study, the performance of anammox granules in presence of OM was evaluated under different COD to N ratios. Low OM concentration did not affect ammonia and nitrite removal significantly but improved the total nitrogen removal via denitrifiers. High OM could suppress anammox activity, resulting in a lower ammonia removal. PCR tests revealed that there was a reduction in the number of anammox bacteria and denitrifiers quantity increased when 400 mg COD/L influent was applied. A COD to N threshold ratio for anammox inhibition, defined when ammonia removal dropped to 80%, was 3.1, higher than that of flocculent sludge. This study revealed that the coexistence of denitrification and anammox was an effective strategy to treat wastewaters containing high levels of nitrogen and OM. (C) 2012 Elsevier Ltd. All rights reserved.