Abstract Putaminoxin E, a natural nonanolide, and its C-9 epimer were synthesized for the first time starting from pentane-1, 5-diol and butyraldehyde. The synthetic sequences involve Maruoka asymmetric allylation, Sharpless kinetic resolution, and ring-closing metathesis as the key steps. The cytotoxic and antimicrobial activities of these compounds were evaluated.