Strongly spin-polarized C-13 NMR lines have been observed upon photoexcitation of FMN-binding LOV domains from the blue-light receptor phototropin. Their origin can be rationalized in terms of intermediate radical-pair spin chemistry. Due to hyperfine-selective branching into singlet and triplet products of different lifetime, nuclear spin polarization builds up on nuclei that possess high electron-spin density in the radical state. By examining point-mutated LOV domains of phototropin, spin-polarized C-13 NMR signals in emission arising from 13C nuclei at natural abundance in the apoprotein can be unambiguously assigned to a tryptophan residue that is located at a distance of about 14 angstrom from the FMN cofactor and that undergoes photoinduced electron transfer to the flavin. This demonstrates the potential of photo-CIDNP in unraveling reactive intermediates in protein function.