A type III polyketide synthase (PKS) cDNA and the corresponding gene (FmPKS) were isolated from the rhizomes of Fallopia multiflora (Thunb.) (Polygonaceae). The full-length FmPKS cDNA was 1,228 bp, containing an open reading frame of 1,137 bp encoding a 378 amino acid residues long protein. The coding sequence of the gene was interrupted by three introns, a different gene structure from most of the type III PKS genes studied so far containing only one intron at a conserved site, except for the recently cloned gene PcPKS2 from Polygonum cuspidatum. Phylogenetic analysis revealed that it shares a close relationship with Rheum tataricum stilbene synthase and formes a group with functionally diverse chalcone synthase-like enzymes. Southern blotting showed that there are three to four copies of the FmPKS gene in the genome. The expression pattern of the FmPKS transcript was determined by Northern blotting and high expression levels were detected in rhizomes and old stems, while the lowest levels were found in old leaves, a pattern that strongly correlates with the accumulation of the major bioactive principles called 2,3,5,4'-tetra-hydroxy-stilbene-2-O-beta-D-glucoside, suggesting that FmPKS might play an important role in its biosynthesis.