Incubation of fluorescein 5'-isothiocyanate (FITC) with soybean lipoxygenase produces the coupling of 1 mol of fluorophore to 1 mol of enzyme. Derivatized lipoxygenase lost 40% activity through a mixed-type inhibitory mechanism. The quenching by IK of the fluorescence of FITC-labeled lipoxygenase shows that the fluorophore is located near the surface of the protein. The partial impediment of the FITC labeling when the substrate is present in the medium, together with data of the tryptic digestion, suggests that FITC is attached via the access channel of substrate to the catalytic site. Labeling does not induce appreciable modification of the enzyme specificity, suggesting that the position of substrate in the active site is not modified by the labeling. The results obtained strongly suggest that FITC labels soybean lipoxygenase specifically at a lysyl residue which contributes to fixation of the carboxylic end of the substrate to the active center. The experimental data obtained from the quenching of FITC fluorescence by NDGA reveal that this molecule interacts with the protein near the catalytic site.