Catalytically active monoamine oxidase (MAO) is believed to exist as a dimer with each subunit containing a covalently attached flavin cofactor. Fluorescence spectroscopy performed on the resting state enzyme resulted in two separate fluorescence emissions at 480 nm and 530 nm with excitation maxima at lambda ex = 412 nm and lambda ex = 450 nm, respectively. Inactivation of MAO with pargyline resulted in concomitant loss of the absorbance at 450 nm without change in the 412 nm absorption; there also was a decrease in the emission intensity at 530 nm, while the emission at 480 nm remained unchanged. The 480 nm emission decreased and the 530 nm emission intensity increased, when the enzyme was heat denatured in the presence of NaDodSO4. From these results, it is clear that there are two different chromophores present in the resting state enzyme; the 530 nm chromophore is consistent with an oxidized flavin, while the 480 nm chromophore could be a flavin semiquinone.