Two sequencing batch reactors were synchronously operated to investigate the effect of manganese (II) (Mn2+) augmentation on aerobic granulation. Reactor 1 (R1) was added with 10 mg/L Mn2+, while there was no Mn2+ augmentation in reactor 2 (R2). Results showed that R1 had a faster granulation process than R2 and R1 performed better in chemical oxygen demand (COD) and ammonium nitrogen (NH (4) (+) -N) removal efficiencies. Moreover, the mature granules augmented with Mn2+ behaved better on their physical characteristics and size distributions, and they also had higher production of extracellular polymeric substances (EPS) content. The result of three-dimensional excitation and emission matrix fluorescence showed that Mn2+ had the function of causing organic material diversity (especially proteins diversity) in EPS fraction from granules. Polymerase chain reaction and denaturing gradient gel electrophoresis techniques were employed to analyze the microbial and genetic characteristics in mature granules. The results exhibited that Mn2+ augmentation was mainly responsible for the higher microbial diversity of granules from R1 compared with that from R2. Uncultured sludge bacterium A16 (AF234726) and Rhodococcus sp. WTZ-R2 (HM004214) were the major species in R1, while only uncultured sludge bacterium A16 (AF234726) in R2. Moreover, there were eight species of organisms found in both two aerobic granules, and three species were found only in aerobic granules from R1. It could be concluded that Mn2+ could enhance the sludge granulation process and have a key effect role on the biological properties during the sludge granulation.