The molecule biological techniques DGGE, clone and real-time PCR were utilized to study primarily the microorganism in 2 anaerobic ammonia oxidation reactors. The results of DGGE showed that despite the seeded sludges in these two reactors were different, but in these two reactors, the microorganism species group structure was similar basically through more than one-year continuous operation. The Planctomycetales clone results showed that the similar 15 sequences (> 99%) had greater distance (< 92%) with the reported sequences of 3 kinds of anaerobic ammonia oxidation bacteria; while they had 97% similar with the KSU-1 sequence which possessed anaerobic ammonia oxidation function. The amoA gene clone results showed that part of the bacteria in the reactor belonged to Nitrosomonas in β-Ptoteobacteria, which possessed the anaerobic ammonia oxidation activity. The results of real-time PCR showed that the anaerobic ammonia oxidation bacteria occupied 27%-29% of the bacteria total amount, the aerobic ammonia oxidation bacteria occupied only 5%.