The phytotoxicity of aluminum ions to rice (Oryza sativa) can be alleviated by ammoniumn compared with nitrate. However, the exact mechanisms underlying this phenomenon are poorly understood. The membrane surface zeta(ζ) potential plays an important role in aluminum adsorption on plant roots and consequently affects aluminum toxicity. Here, the responses of membrane surface ζ potential of isolated protoplasts from rice root tips to ammonium, nitrate, aluminum and pH were examined. It was shown that, ammonium and nitrate themselves did not change the membrane surface ζ potential regardless of Al stress or not. However, both low pH and more Al could significantly depolarize membrane surface ζ potential. Because ammonium could decrease but nitrate could increase medium pH, we concluded that the decreased medium pH induced by ammonium uptake by rice roots depolarized the membrane surfaceζ potential and thereby alleviated rice Al toxicity compared with nitrate.