Two isoenzymes of glucoamylase secreted by strain of Rhizopus microsporus var.chinensis were separated from each other by Native Prep Cell.Three factors including electrophoretic buffer system,gel composition and gel height were investigated.Results indicated when experimental conditions were as follows:Ornstein-Davis electrophoretic buffer system for ionophortic separation,0.02 mol/L,pH 6.2 NaAc·CH3COOH washing system for protein elution,7% gel composition and 6cm gel height for Native PAGE,two isoenzymes with very similar characters could be separated by their different electrophoretic mobility.Moreover,the two isoenzymes maintained their activities after electrophoresis,which contributed to the characterization of the properties of purified proteins.