Epothilones, potent cytotoxic agents and potential anticancer drugs, are complex polyketides produced by a modular polyketide synthase (PKS). The epothilone PKS genes were introduced and expressed in Myxococcus xanthus and engineered to generate novel unnatural natural products which can be used as new scaffolds for chemical modification. Inactivation of the KR domain in module 6 of the epo PKS resulted in accumulation of 9-oxoepothilone D and its isomer 8-epi-9-oxoepothilone D as the major products. Modification of the KR domain in module 4 resulted in the production of the expected compound 12,13-dihydro-13-oxoepothilone C in trace amounts, and the unexpected compound 11,12-dehydro-12,13-dihydro-13-oxoepothilone D as the major product. The other expected compound, 12,13-dihydro-13-oxoepothilone D, was not detected. The unexpected 13-oxo derivative produced indicates that the ER domain of module 5 has substrate-specificity requirements and suggests a second enzymatic role for the domain.