The flavonoid extract from Erigeron breviscapus, breviscapine, has increasingly been used totreat cardio- and cerebrovascular diseases in China for more than 30 years, and plant supplyof E. breviscapus is becoming insufficient to satisfy the growing market demand. Here wereport an alternative strategy for the supply of breviscapine by building a yeast cell factoryusing synthetic biology. We identify two key enzymes in the biosynthetic pathway (flavonoid-7-O-glucuronosyltransferase and flavone-6-hydroxylase) from E. breviscapus genome andengineer yeast to produce breviscapine from glucose. After metabolic engineering andoptimization of fed-batch fermentation, scutellarin and apigenin-7-O-glucuronide, two majoractive ingredients of breviscapine, reach to 108 and 185 mgl –1 , respectively. Our study notonly introduces an alternative source of these valuable compounds, but also provides anexample of integrating genomics and synthetic biology knowledge for metabolic engineeringof natural compounds.