Modular polyketide synthases (PKSs) are well known to use ketosynthase (KS)-driven carbon-carbon bond formation, dehydratase-mediated dehydration to form double bonds, and product release by thioesterase (TE), all of which are regarded as the "canonical" roles for most polyketide biosyntheses. FR901464 is biosynthesized by a complex acyltransferase-less PKS system involving a nonterminal TE domain and several mutated KS domains. Here we demonstrate that this TE catalyzes the dehydration of the polyketide intermediate to yield a cis-double bond and a mutated KS transfers the nascent polyketide chain with only a cis-double bond to the downstream acyl carrier protein. These findings not only provide new insights into different enzymatic functions of PKS domains but also suggest an alternative strategy for cis-double bond formation during the polyketide assembly line.