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Background and aims Silicon (Si) was suggested to enhance plant resistance to toxic elements, and its beneficial role was mainly based on external and internal plant mechanisms. This work aimed at investigating the internal effect of Si on zinc (Zn) detoxification to rice (Oryza sativa L., cv. Tian You 116) seedlings. Methods In a hydroponic experiment, we examined the uptake, xylem loading and localization of Zn in rice seedlings under the condition of 200 μM Zn contamination with the additional silicate supply at three levels ( 0, 0.5 and 1.8 mM).Results The silicate addition significantly increased the seedling biomass, and decreased Zn concentration in both root and shoot of seedlings and in xylem sap flow. Zinpyr-1 fluorescence test and Energy-dispersive X-ray spectroscopy analysis showed the concentration of biologically active Zn 2+ decreased, and Zn and Si co-localized in the cell wall of metabolically less active tissues, especially in sclerenchyma of root. The fractionation analysis further supported silicate supply increased about 10% the cell wall bound fraction of Zn. Conclusions This study suggests the Si-assisted Zn tolerance of rice is mainly due to the reduction of uptake and translocation of excess Zn, and a stronger binding of Zn in the cell wall of less bioactive tissues might also contribute to some degree.