We have determined the crystal structure of NAD(P)H:FMN oxidoreductase, FRasel, from Vibrio fischeri by the multiple isomorphous replacement method at 1.8A resolution. The crystal structures of FRasel complexed with several inhibitors have been also determined. Comparison of these crystal structures suggests that this enzyme recognizes inhibitors by induced-fit and that Phe124 residue of FRasel is essential for their binding. Superposing the active sites of two flavin reductases, FRasel from Vibrio fischeri and FRP from Vibrio harveyi, it seems that these two enzymes have a different pyridine nucleotide binding motif.