Isoflavonoids are very valuable secondary metabolites primarily produced in leguminous plants. They have significant health benefits for humans. As phytoalexins, they play important roles in plant defense against microorganisms. Medicarpin, the major isoflavonoid phytoalexin in alfalfa responding to fungal pathogen attack, is synthesized via the isoflavonoid branch of phenylpropanoid metabolism. There are several enzymes involved in this biosynthetic process. To improve our understanding of this biosynthetic pathway in detail, we are investigating the three dimensional structures of these enzymes, the interactions with their substrates/co-factors, and their catalytic mechanisms.