Understanding defence pathways of plants is crucial to develop disease-resistant agronomic crops, an important element of sustainable agriculture. For this reason, natural plant defenses such as phytoalexins, involved in protecting plants against microbial pathogens, have enormous biotechnological appeal. Crucifers are economically important plants, with worldwide impact as oilseeds, vegetables of great dietetic value and even nutraceuticals. Notably, the intermediates involved in the biosynthetic pathways of unique cruciferous phytoalexins such as rapalexin A and isocyalexin A remain unknown. Toward this end, using numerous perdeuterated compounds, we have established the potential precursors of these unique phytoalexins and propose for the first time their detailed biosynthetic pathway. This pathway involves a variety of intermediates and a novel amino acid as the central piece of this complex puzzle. This work has set the stage for the discovery of enzymes and genes of the biosynthetic pathway of cruciferous phytoalexins of unique scaffolds.