Shikonin biosynthesis in cell suspension cultures of Lithospermum erythrorhizon, which fails to occur under either white or blue light, proved to be strongly inhibited by lumiflavin, a photodegradation product of flavin mononucleotide (FMN). A study on the structure-activity relationship showed that the isoalloxazine moiety is essential for the inhibition of shikonin biosynthesis. These results, as well as the accumulation of biosynthetic precursors, p-hydroxybenzoic acid and its O-glucoside, in the cells irradiated with light, suggest that light would inactivate a flavoprotein necessary for an enzymatic oxidation process leading to shikonin by decomposing the co-factor FMN into lumiflavin.