AbstractPhototropin (phot) is a blue‐light receptor in plants. The protein molecule has two FMN (Flavin MonoNucleotide) binding domains named LOV (Light‐, Oxygen‐, and Voltage‐sensing), which is a subset of the PAS (Per‐Arnt‐Sim) superfamily. Illumination of the phot‐LOV domains produces a covalent C(4a) flavin‐cysteinyl adduct (S390 intermediate)viaa triplet‐excited state, which reverts to the original state in the dark. Chemical structure of the S‐H group of the reactive cysteine is important for the adduct formation, and several models have been proposed for efficient reaction. By means of Fourier‐transform infrared (FTIR) spectroscopy of the LOV2 domain ofAdiantumphytochrome3 (phy3‐LOV2), a fusion protein of phot containing the phytochrome chromophoric domain, we have studied protonation state of the reactive cysteine (Cys966). Although it was proposed that the cysteine is deprotonated in LOV domains, we observed an S‐H stretch at ˜2570 cm−1. Since phy3‐LOV2 possesses only one cysteine at position 966, this observation clearly indicates that Cys966 is protonated. While transfer reaction of proton, hydrogen, or electron has been proposed from the cysteine in the triplet‐excited state, we also detected the S‐H stretch at 2537 cm−1in the triplet‐excited state of phy3‐LOV2. This excludes the possibility of proton and hydrogen transfer reactions. These frequencies imply that the S‐H group is free from hydrogen bond in the unphotolyzed state, while it forms a strong hydrogen bond in the triplet‐excited state. We infer the hydrogen‐bonding acceptor to be the N(5) atom of FMN, and such strong interaction presumably driv