High-rate denitrification is a popular and efficient process for treatment of nitrate-rich wastewater. Knowing the effect of heavy metals on denitrification is essential for industrial development. In the present study, the long-term impacts of Zn(II) on denitrifying granular sludge were investigated. The suppression threshold of Zn(II) on denitrifying bacteria was 10 mg L-1 for long-term exposure. The nitrogen removal rate was decreased by long-term addition of 10 mg L-1 Zn(II). Castellaniella and Klebsiella were the two dominant genera under Zn(II) stress. The relative abundance of Klebsiella sharply decreased to 4.64% after the addition of 10 mg L-1 Zn(II), whereas Castellaniella was susceptible to 2 mg L-1 Zn(II), revealing that Castellaniella mainly was devoted to denitrification under no or low Zn(II) stress conditions, whereas Klebsiella was effective under high Zn(II) stress.