Abstract: Scanning electron microscope （SEM） and fluorescence in situ hybridization （FISH） were used to study the bacterial morphology and community of the complete autotrophic nitrite-nitrification and electrochemical bio-denitrification combined process （CANNED）, which was operated for ammonium wastewater treatment at different influent concentrations of free ammonia （FA）. When the mass concentration of FA was 0.5 mg/L in the nitrite-nitrification part, the AOB and NOB were 0.9% and 2.8% of the bacteria, respectively. It could achieve short-term nitrification when the mass concentration of FA was 12.4-48.6 mg/L. AOB and NOB were 33.6%-47.4% and 1.0%-2.9% of bacteria respectively under the above mentioned conditions. In the electrochemical bio-denitrification part, the thiobacillus denitrificans, anammox bacteria and eubacteria were 7.2%-15.3%, 7.2%-10.3% and 9.1%-14.3% of total bacteria respectively when the influent FA was 0.5-12.4 mg/L. When the mass concentration of FA increased to 48.6 mg/L, the above three kinds of bacteria were 34.5%, 44.2% and 60.8% of total bacteria respectively, which indicated that the growth of the bacteria was accelerated with the concentration of FA increasing. The above mentioned results were in accordance with the SEM results.