One of the approaches of combinatorial biosynthesis is combining genes from different organisms and designing a new set of gene clusters to produce bioactive compounds, leading to diversification of both chemical and natural product libraries. This makes efficient use of the potential of the host organisms, especially when microorganisms are used. An Escherichia coli system, in which artificial biosynthetic pathways for production of plant-specific medicinal polyketides, such as flavonoids, stilbenoids, isoflavonoids, and curcuminoids, are assembled, has been designed and expressed. Starting with amino acids tyrosine and phenylalanine as substrates, this system yields naringenin, resveratrol, genistein, and curcumin, for example, all of which are beneficial to human health because of their wide variety of biological activities. Supplementation of unnatural carboxylic acids to the recombinant E. coli cells carrying the artificial pathways by precursor-directed biosynthesis results in production of unnatural compounds. Addition of decorating or modification enzymes to the artificial pathway leads to production of natural and unnatural flavonols, flavones, and methylated resveratrols. This microbial system is promising for construction of larger libraries by employing other polyketide synthases and decorating enzymes of various origins. In addition, the concept of building and expressing artificial biosynthetic pathways for production of non-bacterial and unnatural compounds in microorganisms should be successfully applied to production of not only plant-specific polyketides but also many other useful compound classes.