Primary metabolism supports essential chemical processes of living organisms, and is highly conserved among all life forms. In contrast, specialized metabolism contributes to the fitness of its host in specific abiotic and biotic environments, and distributes taxonomically along the evolving tree of life. We seek to understand how complex specialized metabolites are biosynthesized through an assembly line of specialized enzymes, why these specialized metabolic traits are relevant to their hosts under ecological niches, and how these complex pathways could have evolved in a Darwinian fashion. Exploration of the largely untapped eukaryotic specialized metabolic systems not only will advance our understanding of the chemistry of life processes, but also will empower synthetic biologists to engineer microbial production of those high-value natural products of eukaryotic origin in the near future.