The regioselective acylation of naturally occurring plant pigments with aromatic acids such as caffeic acid and p-coumaric acid was examined by an enzymatic reaction system from cultured cells of Ipomoea batatas. Isoquercitrin, a flavonoid glucoside, was converted to isoquercitrin 6''-O-caffeate by the enzymatic system. Chrysanthemin, an anthocyanin, was also acylated to the corresponding caffeate ester. This enzymatic method should prove useful for the synthesis of acylated flavonoid glucosides such as isoquercitrin caffeate, whose productivity is low using lipase-catalyzed transesterification.