In order to reveal the biological diversity and the evolution of microbial community structure in the process of sludge cultivation and acclimation at the start-up stage of simultaneous partial nitrification and denitrification (SNAD) process, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the microbial community structure in different operating periods. And molecular cloning was used for species identification and phylogenetic analysis. The 16S rDNA sequence analysis of the characteristic bands of the DGGE profile of total bacteria showed that the bacterial populations in the sludge were rich in diversity, and β- proteobacteria were slightly more abundant and maintained a relatively stable dominant position. With the operation of the reactor, the secondary populations were strengthened and became new dominant communities, such as Firmicutes, γ- proteobacteria, Bacteroides and so on. The 16S rDNA sequence analysis of the characteristic bands of the DGGE profile of ammonia-oxidizing bacteria showed that the strains obtained by sequencing basically belonged to Nitrosomonas of β-proteobacteria. The fast growth rate of this genus made it the dominant ammonia-oxidizing bacteria (AOB) in the activated sludge systems.