Completely autotrophic nitrogen removal over nitrite (CANON) has been regarded as an efficient and economical process for nitrogen removal from wastewater. The distribution and genetic diversity of the functional microorganisms in five lab-scale CANON reactors have been investigated by using some molecular biology methods. Nitrosomonas-like aerobic ammonium oxidizing bacteria (AerAOB) and Candidatus Brocadia-related anaerobic ammonium oxidizing bacteria (AnAOB) were detected as predominant functional microbes in the five reactors while Nitrobacter-like nitrite oxidizing bacteria (NOB) existed only in the systems operated at ambient temperature. Communities of AerAOB and AerAOB were almost similar among the five reactors while the distribution of the functional microbes was either scattered or densely packed. Meanwhile, this study has demonstrated the feasibility of starting up CANON by inoculating conventional activated sludge in low ammonium content at ambient temperature. (C) 2012 Elsevier Ltd. All rights reserved.