This contribution primarily addresses formation of the plant-protecting and human health-protecting lignans found in flax seed coat tissue. Yet, the fundamentals of how plants in general biochemically produce their protective seed coats (protecting the embryo until germination) are very poorly understood at the molecular level, in spite of its massive evolutionary importance. Flax is no exception. Herein, we address the natural product molecular species produced from the “mixed” biochemical pathways to both the flax seed lignans and other metabolite classes associated with same, as well as what is known about their localization in situ and their biosynthesis (proteins and enzymes involved). The biosynthetic pathway known to this point to the plant defense lignans in leaf and stem tissue is also discussed. Discovery of the biochemical steps leading to flax seed coat lignan biosynthesis is described, with a particular emphasis on the genes, dirigent proteins (DPs), downstream pinoresinol-lariciresinol reductases, and secoisolariciresinol dehydrogenase. Advances made thus far from X-ray structural biology investigations, as well as MALDI TOF MS/MS and Ion Mobility metabolite imaging, of these biochemical processes to the lignan components in situ are also summarized. While the predominant health-protecting flax seed coat lignans are secoisolariciresinol diglucoside (SDG) derived, they are essentially not present as such in this tissue. Instead, SDG exists in covalently linked form to other “mixed” biochemical pathway metabolites, of which there are currently eight other distinct natural product entities considered to be involved. The biosynthesis of the other components, such as herbacetin diglucoside and 3-hydroxy-3-methylglutaric acid, is also briefly mentioned. Moreover, our knowledge of the macromolecular structure(s) of these lignan-containing mixed biochemical pathway metabolites during seed coat maturation is briefly summarized. Flaxseed, however, also contains other lignans, such as pinoresinol, pinoresinol diglucoside, isolariciresinol, and matairesinol, albeit in tiny amount, which are released on alkali (base) treatment of flax seed or preparations thereof. The lignan yatein, by comparison, accumulates in flax leaf and stem tissue and appears to be involved in plant defense. What is known about its biochemical pathway and function is summarized. Interestingly, flax DPs are encoded by a 44-membered multi-gene family, of which only a few are of known biochemical/physiological function. Future research is urgently needed to ascertain the in vivo functions of this DP family, including probing the evolutionary ramifications of same and their relevance to successful evolutionary transition of aquatic plants to terrestrial vascular plant form.