Brassilexin and sinalexin are among the most potent antifungal phytoalexins produced by crucifer plants. Nonetheless, the crucifer pathogen Leptosphaeria maculans (Desm.) Ces. et de Not. (asexual stage Phoma lingam (Tode ex Fr.) Desm.) is able to detoxify these phytoalexins. To understand and control these reactions, the elusive brassilexin and sinalexin detoxification pathways in L. maculans were investigated and compared to those of the synthetic derivatives 8-methylbrassilexin and 8-acetylbrassilexin. The chemical structures, syntheses and antifungal activities of the metabolic intermediates, including the most polar metabolite identified thus far, 3-formylindolyl-2-sulfonic acid, were established. Our overall findings suggest that the first detoxification step of brassilexin involves its reductive bioconversion to 3-aminomethyleneindole-2-thione, followed by hydrolysis and oxidation to the water soluble metabolite 3-formylindolyl-2-sulfonic acid.