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Terpenoids are the largest class of natural products and are derived from C5 isoprene units. Recent discoveries of modification enzymes in native isoprene units before cyclization or transfer reactions have revealed that C5 units with additional carbon atoms are also used to produce terpenoids. These reports indicate that the utilization of these modification enzymes is useful for the enzymatic production of non-natural terpenoids. In this study, we have attempted to produce methylgeranyl polyphenols, which are not observed in nature, by combining a geranyl pyrophosphate C6 methyltransferase, BezA, which was discovered from the benzastatin biosynthetic pathway, and the promiscuous prenyltransferase NphB, which catalyzes prenylation of various flavonoids. We successfully synthesized five methylgeranylated flavonoids from naringenin, apigenin, and genistein. This result demonstrates that BezA is a powerful tool for the synthesis of novel non-natural terpenoids.