The initial kinetics for the syntheses of N-(benzyloxycarbonyl)-L-alanyl-L-phenylanine methyl ester (ZAPM) and N-(benzyloxycarbonyl)-L-aspartyl-L-phenylalanine methyl ester (ZDPM) in an aqueous/organic biphasic system, using free thermolysin were elucidated, both experimentally and theoretically. As model organic solvents, ethyl acetate and tert-amyl alcohol were used. The substrate concentration dependencies of the initial rate of syntheses for ZAPM and ZI)PM observed in the biphasic system were well simulated using the overall partition coefficients of the substrates and product taking into consideration the effect of the formation of ion-pair complexes between the acid and amine components of the substrate, the initial rate equations determined in an aqueous buffer saturated with the organic solvent, and the pH dependence of the rate constant. The equilibrium yield for the synthesis of ZDPM was also in good agreement with the calculated result using the overall partition coefficients and equilibrium constant measured in the aqueous buffer.