Aluminum (Al) and manganese (Mn) toxicity are two main constraints to crop production in some acid soils. In the present study, hydroponic experiments were conducted to investigate the phytoxicity caused by the metals Al and Mn in the Al-sensitive soybean (Glycine max) cultivar Jilin62. Results showed that more than 80% of the total cellular Al accumulated in the cell walls of the root tissue. Excessive Mn supply significantly increased the Al level in the root and aggravated Al toxicity, and as the result leading to a stronger inhibition of the root-elongation rate and root-biomass production. No obvious change of Al concentration was detected in root-cell organelles and soluble fractions. Interestingly, Al-induced increase in cell wall pectin content in the root was further enhanced by addition of Mn, which might explain how Mn aggravated Al toxicity. In addition, it was found that high levels of Al significantly alleviated Mn toxicity symptoms like brown spots on the old leaves, crinkle on the young leaves and shoot growth inhibition. This Al reduced Mn toxicity was related to the decrease of Mn content in shoots under combined Al and Mn stress. Lanthanum (La3+), which has similar chemical properties as Al, can also reduce Mn toxicity and Mn accumulation in the plant. Thus, it is speculated that Al exerts an antagonistic effect on Mn uptake, and thus leads to alleviated Mn toxicity.