In order to investigate the correlation between reactor performance and the microorganisms, an integrated A/O reactor was operated for 72 days to treat diluted livestock wastewater. Chemical oxygen demand (COD) removal efficiency increased from 79% to 94%,with total nitrogen (TN) removal efficiency from 37% to 50% (HRT 7.4 hr) when the influent COD and TN were ca. 1500 mg/L and 95 mg/L, respectively, and the outlet COD concentration was less than 100 mg/L at the end. Microbial community was monitored during start-up period by denaturing gradient gel electrophoresis (DGGE) based on 16S rRNA gene. DGGE profiles showed that microbial community had changed significantly during the start-up and these shifts were in accordance with the reactor performance. UPGMA clustering analysis showed that 14 anaerobic samples fell into five main groups and so did the aerobic ones, but the grouping patterns were different. Phylogenetic analysis indicated that microbial populations in the anaerobic compartment belonged to Firmicutes,Proteobacteria, Chloroflexi and Bacteroidetes, while Proteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobiae and Nitrospira were present in the aerobic compartment. In the anaerobic compartment, more fermentative and acetogenic bacteria were detected during the start-up while denitrifying bacteria faded away. Two functional populations such as Nitrospira defluvii and Dechloromonas denitrificans were observed when nitrogen removal was high, indicating that simultaneous nitrification and denitrification occurred in the aerobic compartment.