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S-Alk(en)yl- l-cysteine sulfoxides are cysteine-derived secondary metabolites highly accumulated in the genus Allium. Despite pharmaceutical importance, the enzymes that contribute to the biosynthesis of S-alk-(en)yl- l-cysteine sulfoxides in Allium plants remain largely unknown. Here, we report the identification of a flavin-containing monooxygenase, As FMO1, in garlic ( Allium sativum), which is responsible for the S-oxygenation reaction in the biosynthesis of S-allyl- l-cysteine sulfoxide (alliin). Recombinant As FMO1 protein catalyzed the stereoselective S-oxygenation of S-allyl- l-cysteine to nearly exclusively yield ( RC SS)- S-allylcysteine sulfoxide, which has identical stereochemistry to the major natural form of alliin in garlic. The S-oxygenation reaction catalyzed by As FMO1 was dependent on the presence of nicotinamide adenine dinucleotide phosphate (NADPH) and flavin adenine dinucleotide (FAD), consistent with other known flavin-containing monooxygenases. As FMO1 preferred S-allyl- l-cysteine to γ-glutamyl- S-allyl- l-cysteine as the S-oxygenation substrate, suggesting that in garlic, the S-oxygenation of alliin biosynthetic intermediates primarily occurs after deglutamylation. The transient expression of green fluorescent protein ( GFP) fusion proteins indicated that As FMO1 is localized in the cytosol. As FMO1 mRNA was accumulated in storage leaves of pre-emergent nearly sprouting bulbs, and in various tissues of sprouted bulbs with green foliage leaves. Taken together, our results suggest that As FMO1 functions as an S-allyl- l-cysteine S-oxygenase, and contributes to the production of alliin both through the conversion of stored γ-glutamyl- S-allyl- l-cysteine to alliin in storage leaves during sprouting and through the de novo biosynthesis of alliin in green foliage leaves. [ABSTRACT FROM AUTHOR]