Treatment of soybean lipoxygenase isozyme 1 with its substrates, linoleic acid and oxygen, or product, 13(S)-hydroperoxy-9,11(Z,E)-octadecadienoic acid (13-HPOD), leads to the appearance of a purple color. Although the structure of the chromophore has not been determined, we present strong evidence that it is an Fe(3+)-OOR complex between the enzyme and 13-HPOD. Irradiation of frozen purple solutions of lipoxygenase causes the reversible production of a radical, shown by the effects of 2H and 17O enrichment on its EPR spectrum to be derived from 13-HPOD. The action spectrum of the photolysis reaction corresponds to the visible spectrum of the purple species, strongly implying that the purple chromophore contains 13-HPOD (or a product thereof) as part of its structure. Concomitant with the production of this radical there is a decrease in the intensity of an EPR signal corresponding to enzyme-bound Fe3+ and characteristic of the purple species. Taken together, these observations support the suggestion that the purple species is a complex between ferric lipoxygenase and 13-HPOD, likely the ferric peroxide.