The effects of excess boron (B) on some physiological and nutritional parameters of two distinctive quince (Cydonia oblonga Mill.) rootstocks were investigated. Throughout the world, B toxicity is a widely faced problem of soil in arid and semi-arid environments. In a greenhouse study, boron was applied at the rates of 0 and 40 mg kg(-1) soil to quince A and quince C rootstocks. Toxicity of B differentially affected studied parameters and rootstocks. Boron toxicity increased B concentrations of both rootstocks however the increase was more pronounced in quince A rootstock. SPAD readings, (SPAD-meter, Minolta 502 Co Ltd., Japan) as a measure of chlorophyll decreased under B toxicity. Boron toxicity increased membrane permeability and anthocyanin in both rootstocks. Although, there is rootstocks difference, lipid peroxidation (MDA) and proline and TAA (non-enzymatic total antioxidant activity) increased in response to B toxicity. In general, quince C had lower MDA (Malondialdehyde) and TAA but lower level of proline as compared to quince A. Boron toxicity did not affect the concentrations of P, Ca, Zn and Cu however increased B and Mn concentrations. Magnesium (Mg), Mn and Fe concentrations of quince were found higher than that of quince C. Indicating a genotypic effect, quince A and quince C responded to B toxicity differentially.