Molecular mechanism of fluorescence quenching of flavins in flavodoxin from Desulfovibrio vulgaris, strain Miyazaki, and riboflavin binding protein from egg white has been investigated by means of picosecond laser photolysis technique. In the case of flavodoxin, a transient absorption band characteristic of the non-fluorescent exciplex formed by electron transfer from indole to excited flavins in model systems has been observed around 600 nm at the delay time of 33 ps from exciting ps pulse pulse width, 25 ps). In the case of riboflavin binding protein, the transient absorption spectra were different from those of flavin-indole exciplex and rather similar to the spectra of the model system of flavin-phenol. These results suggest that tryptophan residue exists near the isoalloxazine nucleus in flavodoxin, and in riboflavin binding protein, tyrosine residue exists near the flavin. Direct measurements of the ultrafast process of the electron transfer in flavoproteins as developed here could provide useful information for elucidating protein dynamics, associated with redox reaction, in the picosecond time region.