Cell hydrophobicity is an important affinity force in cell self-immobilization and attachment processes. The role of cell hydrophobicity in the formation of aerobic granules has. not been clear. Therefore, two series of experiments were conducted to investigate the role of cell hydrophobicity in the formation of aerobic heterotrophic and nitrifying granules in sequencing batch reactors, while the effects of shear strength, hydraulic selection pressure, and organic loading rate on the cell hydrophobicity were also studied. Results showed that the formations of heterotrophic and nitrifying granules were associated very closely with the cell hydrophobicity. The hydrophobicity of granular sludge was nearly twofold higher than that of conventional bioflocs. A high shear force or hydraulic selection pressure imposed on microorganisms resulted in a significant increase in the cell hydrophobicity, while the cell hydrophobicity seemed not to be sensitive to the changes in the organic loading rates in the range studied. In conclusion, the cell hydrophobicity could induce and further strengthen cell-cell interaction, and might be a main triggering force to initiate the granulation of heterotrophic and nitrifying bacteria.