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This study investigates microbial population dynamics in granular sequencing batch reactors (GSBR). The experimental results of DGGE fingerprint of sludge demonstrated that the microbial community structure of sludge shifted significantly during granulation period and nutrient removal improvement period. After reactor performance and physical characteristics of sludge reached steady state, microbial population of sludge became relatively stable. The high similarity of microbial community structure between co-existed flocculated sludge and granular sludge in GSBR at different operation phases indicated that similar microbial consortium could exist in compact aggregated form or in amorphous flocculated form. Therefore, strong selection pressure was still required to wash out flocs to maintain the stability of reactor operation. In addition, it was found that substrate type had considerable impact on microbial species selection and enrichment in granular sludge. The clone library of granular sludge showed that microbial species in divisions of α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria and Bacteroidetes existed within acetate-fed granule communities and Thauera spp. from β-Proteobacteria accounted for 49% of the total clones in the whole clone library. It is thus speculated that Thauera spp. are important for the formation of acetate-fed granules under the conditions used in this study, maintaining the integrity of granules or substrate degradation.