<jats:title>Abstract</jats:title><jats:p>The flavonoid extract from<jats:italic>Erigeron breviscapus</jats:italic>, breviscapine, has increasingly been used to treat cardio- and cerebrovascular diseases in China for more than 30 years, and plant supply of<jats:italic>E. breviscapus</jats:italic>is becoming insufficient to satisfy the growing market demand. Here we report an alternative strategy for the supply of breviscapine by building a yeast cell factory using synthetic biology. We identify two key enzymes in the biosynthetic pathway (flavonoid-7-<jats:italic>O</jats:italic>-glucuronosyltransferase and flavone-6-hydroxylase) from<jats:italic>E. breviscapus</jats:italic>genome and engineer yeast to produce breviscapine from glucose. After metabolic engineering and optimization of fed-batch fermentation, scutellarin and apigenin-7-<jats:italic>O</jats:italic>-glucuronide, two major active ingredients of breviscapine, reach to 108 and 185 mg l<jats:sup>–1</jats:sup>, respectively. Our study not only introduces an alternative source of these valuable compounds, but also provides an example of integrating genomics and synthetic biology knowledge for metabolic engineering of natural compounds.