Berberis amurensis Ruprecht(Berberidaceae) is a medicinal plant indigenous to the middle and northern part of Korean peninsula. The woody parts of this plant have been used for the ocular, peptic and intestinal disorders. The stems of this plants were extracted with MeOH and the MeOH extract was partitioned between organic phases and water layer, successively to fractionated quarternary alkaloids. The acetone-soluble part of guarternary alkaloidal fraction had antibacterial activities and it contained four protoberberine alkaloids such as palmatine(I), Berberine(II), Jatrorrhizine(III) and coptisine(IV), and one aporphine alkaloid, magnoflorine(V). Although the isolations of the compounds I, II, IIII, IV and V from different sources were reported, this is the first report that Berberis amurensis contained the compounds. When the contents of compound I(palmatine) and II(berberine) were quantified and compared with those of other plant parts, cortex contained higher palmatine and berberine than any other part of the plant.