This paper was aimed at investigating the bio-augmentation performance of anaerobic/aerobic/ anoxic-type sequencing batch reactor (SBR) during its start-up period by introducing a strain of denitrifying polyphosphate-accumulating organism (DPAO). Two SBR reactors were inoculated to study the start-up performance, with one for DPAO introduction and the other as the control specimen. A comparison, of microbial community diversity based on the reactor which obtained a better performance, was made between polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses encoded by 16S rRNA and functional genes (nirS, nirK). The results indicated that the introduction of DPAO had a positive effect on the biological system, including a reduction of the start-up period, the improvement of sludge characteristics and the removal efficiency of nutrients, especially for phosphorus. By comparing the phylogenetic relationship of 16S rRNA and functional genes (nirS, nirK) of the reactor augmented with DPAO, it could be found that the phylogenetic relationship of these genes were remarkably inconsistent with each other. Therefore, 16SrRNA should not be used to determine the microbial community diversity of functional bacteria which could accomplish denitrification, and gene nirK should not be neglected when determining functional bacteria.