Phy3-LOV2 is the chromophore domain of a blue-light photoreceptor for tropic responses of plants. FMN is noncovalently bound to phy3-LOV2, and the protein structure is characteristic of the LOV (light-oxygen-voltage) domain. Primary photoreaction is considered to be adduct formation between FMN and a cysteine, while deprotonation of the cysteine S-H group was suggested. On the basis of the infrared spectral analysis, however, we have shown that the cysteine of phy3-LOV2 is in the protonated S-H form, and not in the thiolate form in the ground state. Upon formation of S390, the S-H group disappears, presumably forming the adduct between FMN and Cys966. S390 can be trapped at 150 K, and the protein structure of S390 may not be changed drastically at 295 K.