In order to realize effect of different sets of universal primers on the analysis of microbial community of activated sludge based on targeted sequence of 16S rDNA and employ effectively denaturing gradient gel electrophoresis (DGGE), activated sludge were obtained from the continuous stirred tank reactor (CSTR), 16S rDNA fragments were amplified with there primer sets (341f/534r, 968f/1401r and 341f/926r), and the diversity and dynamics of microbial communities were investigated by DGGE. The results indicated that community diversity and dynamics was obviously different based different sets of universal primers by DGGE. Separated patterns of the targeted sequence of primer 341f/534r and 968f/1401r were better than of 341f/926r. The similarity of communities between S2 and S3 was high in the DGGE profiles with primer 341f/534r and 341f/926r, the similarity of communities between S1 and S2 was high in the DGGE profiles with primer 968f/1 401r, it demonstrated that the similarity and dynamics of communities was different each other based different sets of universal primers. In the DGGE profiles, bands and diversity from primer 341f/534r were most, bands and diversity from primer 341f/926r were least. Thereby, while activated sludge was analyzed by DGGE, primers 341f/534r and 968f/1401r were more effective than 341f/926r.