Irradiation of the LOV1 domain from the blue-light photoreceptor phototropin of the green alga Chlamydomonas reinhardtii leads to the formation of a covalent adduct of the sulfur atom of cysteine 57 to the carbon C4a in the chromophore FMN. This reaction is not possible in the mutant LOV1-C57G in which this cysteine is replaced by glycine. Irradiation of LOV1-C57G in the absence of oxygen but in the presence of aliphatic mercaptans or thioethers leads to the formation of a species with an absorption maximum at 615 nm, which is identified as the neutral radical FMNH˙. When oxygen is admitted, the reaction is completely reversible. Irradiation of LOV1-C57G in the presence of methylmercaptan CH3SH under oxygen-free conditions yields, in addition to FMNH˙, a third species with a single absorption maximum at 379 nm. This species is stable against oxygen and is also formed when the irradiation is performed in the presence of oxygen. This species is assigned to the adduct between CH3SH and FMN. In aqueous solution the photoreaction of CH3SH with FMN leads to the fully reduced hydroquinone form FMNH2 or its anion FMNH−. Adduct formation apparently requires the protein cage. After formation, the adduct is stable for hours inside the protein, but decomposes immediately upon denaturation. The implications of these observations for the mechanism of adduct formation in wild type LOV domains are discussed.