Flavin-binding Kelch repeat F-box (FKF1) protein plays important roles in the photoregulation of flowering in Arabidopsis. FKF1 has a light, oxygen, and voltage (LOV) sensing domain binding a flavin mononucleotide (FMN) as a chromophore noncovalently. Photoreaction of the FKF1-LOV polypeptide was studied by low-temperature absorption spectroscopy. Upon blue light irradiation, a ground state, D(450), is converted to S(390) known as a cysteinyl-flavin adduct intermediate in the photoreaction of phototropin. Below 150 K, bleaching of D(450) was much reduced and a new photoproduct, Z(370), appeared as well as S(390) formation. The calculated absorption spectrum for Z(370) is very similar to those of flavoproteins in an anion radical state. On the basis of the results that S(390) formation proceeds to Z(370) formation and that Z(370) formed at low temperatures reverts to D(450) upon temperature increase, Z(370) is concluded to be not an intermediate from D(450) to S(390). Z(370) is suggested to be formed from the biradical triplet-excited state after relaxing to the ground state with the FMN anion radical trapped at the low temperature, in which the SH of the cysteine is in the wrong position that is able to produce a radical pair but unable to form the cysteinyl-flavin adduct. The counter SH in the cationic radical state may revert to the ground state by extracting an electron from the unidentified amino acid residue. Interestingly, S(390) that has been thought to be irreversible to D(450) was revealed to revert to D(450) very slowly with a half-life time of 62.5 h in solution at 298 K. The photoreaction mechanism is discussed in reference to the calculated activation energy of the reaction processes.