This study determined the most effective microbes acting as ammonia-oxidising (AOB) and manganese-oxidising bacteria (MnOB) for the simultaneous removal of ammonia (NH4+-N) and manganese (Mn2+) from water. Two conditions of mixed culture of bacteria: an acclimatised mixed culture (mixed culture: MC) in a 5-L bioreactor and biofilm attached on a plastic medium (stages of mixed culture: SMC) in a biological aerated filter were isolated and identified using Biolog MicroSystem and 16S rRNA sequencing. A screening test for determining the most effective microbe in the removal of NH4+-N and Mn2+ was initially performed using SMC and MC, respectively, and found that Bacillus cereus was the most effective microbe for the removal of NH4+-N and Mn2+. Moreover, the simultaneous NH4+-N and Mn2+ removal (above 95% removal for both NH4+-N and Mn2+) was achieved using a biological aerated filter under various operating conditions. Thus, the strain could act as an effective microbe of AOB and a MnOB for the simultaneous removal of NH4+-N and Mn2+. (C) 2012 Elsevier Ltd. All rights reserved.