On the basis of recent information on the chemical structure of allophane with nano-ball morphology, a new mechanism was proposed for phosphate adsorption on the allophane: replacement of weakly bonded silicon with phosphorus. First experimental ground for the mechanism was linear relationship between silicon release and phosphate adsorption. Second was much more silicon release upon the adsorption for allophane with higher Si/Al ratio which contains much weakly bonded silicon in its chemical structure than for allophane with the low ratio. The replacement mechanism was formulated as: ≡Si-O-Si(OH) 3 + H 2 PO 4 - → ≡Si-O-PO(OH)O - + Si(OH) 4 . Possibility of the reaction was proven by negative value of the change in heats of formation, AH, obtained by molecular orbital calculation. The replacement mechanism is not a kind of usual adsorptions, but regarded as one of chemical reactions between allophane and phosphate. We also found that high phosphate concentration in aqueous solution (>1.5mM) caused partial destruction of allophane structure even around pH 6, and that Ca 2+ ion enhanced phosphate adsorption by bridging effect between allophane and phosphate.