The ultrafast non-exponential fluorescence decay of FMN binding protein (FBP) was analyzed with three electron transfer (ET) theories, Marcus theory, Bixon and Jortner theory and Kakitani and Mataga theory. Center to center distances between electron acceptor, the excited isoalloxazine, and donors, Trp-32, Tyr-35 and Trp-106, in FBP were determined by molecular dynamic simulation. Electron transfer parameters containing in these theories were determined so as to fit the calculated decay with the observed decay, according to a non-linear least squares method. Introduction of electrostatic energies between isoalloxazine anion and other ionic groups and between the donor cations and other ionic groups in the protein into any ET theories improved the fitting. The non-exponential behavior in the fluorescence decay is considered to be ascribed to a fluctuation of the protein structure with long period. © 2008 Elsevier B.V. All rights reserved.