BACKGROUND: This study was conducted to investigate the feasibility and performance of nitrogen removal through the complete autotrophic nitrogen removal over nitrite (CANON) process for saline wastewater in a continuous reactor, and to characterize microorganisms in the sludge from the reactor using DNA-based techniques. RESULTS: The nitrogen removal experiment in the reactor was operated over five phases for 286 days treating a synthetic sewage of 1.2% salinity at 21-25 degrees C. At dissolved oxygen (DO) concentrations of 0.5-1.0mg L-1 and in the presence of glucose, NO2- was accumulated, indicating the activity of ammonia-oxidizing bacteria (AOB). At DO concentration of 0.5mg L-1 without organic substrate, the anaerobic ammonium oxidation (Anammox) process was the major pathway responsible for nitrogen removal, with a total nitrogen removal of 70% and an ammonium conversion efficiency of 96%. Amaximum ammonium removal rate of 0.57 kg-N m(-3) d(-1) was achieved during the experimental period. The concentrations of AOB and Anammox bacteria were monitored over the operation of reactor using quantitative real-time polymerase chain reaction (qRT-PCR). CONCLUSION: In this study, autotrophic nitrogen removal process was achieved under salinity condition in a one-reactor system. An over 100 fold increase of AOB was found due to the increased supply of ammonium at the beginning, then AOB concentration decreased temporarily in correspondence with the decreased DO, and the AOB resumed their concentration at the last phase. The Anammox bacteria abundance was about 150 fold higher than that at the beginning, indicating the successful enrichment of Anammox bacteria in the reactor. (C) 2010 Society of Chemical Industry