It is shown that commercial FMN contains a considerable amount of the 4', 3', and 2' isomers and other phosphorus-containing compounds. These impurities can easily be analyzed and quantified by the 31P NMR technique. The phosphate group of FMN bound to Megasphaera elsdenii apoflavodoxin is probably in the dianionic form. Its chemical shift is almost independent of pH in the range 5.5-9.2 and of the redox state of the protein. The phosphate group of bound FMN is buried in the protein. Protons of the apoprotein and of bound water located in the vicinity of the phosphate group in native flavodoxin are not exchangeable with deuteron of the bulk solvent. These protons are, however, easily exchangeable in apoflavodoxin, as shown by reconstitution experiments. The distance between the phosphorus atom of bound FMN and the N(10) atom of the isoalloxazine moiety of FMN is calculated to be about 7.8 A. This result is in good agreement with X-ray data published for the related flavodoxin from Clostridium MP. The electron exchange between the oxidized and semiquinone state of M. elsdenii flavodoxin is rather slow (kexc' much less than 2 s-1) whereas that between the semiquinone and hydroquinone form is much more favored (kexc' much greater than 100 s-1). This indicates that the activation energy for the transition between the semiquinone and hydroquinone states must be smaller than that for the transition between the oxidized and semiquinone states. These results offer a reasonable explanation for the one-electron transfer reaction of flavodoxins in biological reactions.