Cerulenin, [(2S,3R)-2,3-epoxy-4-oxo-7,10-dodecadienoylamide], a mycotoxin produced by Cephalosporium caerulens, irreversibly inactivated 6-methylsalicylic acid synthase from Penicillium patulum. A combination of radiolabelling studies with [3H]cerulenin, proteolytic and chemical digestion and N-terminal sequencing of labelled peptides indicated that the site of cerulenin modification is the highly reactive substrate-binding Cys-204 of the β-ketoacyl synthase enzyme component. The thiol-specific inhibitor, iodoacetamide, was also shown to alkylate this residue. These findings are analogous with those observed for the reaction of cerulenin and iodoacetamide with type-I fatty acid synthases, demonstrating the close similarity between 6-methylsalicylic acid synthase and type-I fatty acid synthases.