Abstract: In order to find the better method to deal with late landfill leachate, the stable partial nitrification system was operated in the MBR (membrane bioreactor). The microbial community structure of the stable partial nitrification phase was investigated by the total bacterial clone library and the cloning library of ammonia oxidizing bacteria (AOB) functional gene amoA. 82 positive clones were selected randomly from 16S rDNA clone library and their sequence was determined. The results show that there are four dominant bacterium groups in the stable partial nitrification phase:Proteobacteria (64.65%), uncultured bacterium (18.3%), Bacteroidetes (9.76%), and Firmicutes (7.32%). Building on the cloning library of AOB's functional gene amoA, 73 positive clones were selected from the library and their sequence was also determined. Compared with basic local alignment search tool(BLAST), the results show that only the Nitrosomonas and Uncultured bacterium are detected in the system, and their proportion is 41.1% and 58.9%, respectively. This phenomenon show that the number of Nitrosomonas is maximum in this system. At the same time, the existence of many unknown bacterial species showed that there are a large number of microbial resources in the system and needing further development.