Javanicunines A-B and 9-deoxy-PF1233s A-B belong to a family of natural diketomorpholines with a unique isopropenyl group at C-10b or C-5a and a hydroxyl group at C-11a or C-10b. We herein reported the first total synthesis of javanicunines A-B and 9-deoxy-PF1233s A-B. Pivotal features of the synthesis included a nucleophilic substitution reaction, followed by a Davis' oxaziridine oxidation to assemble javanicunines A-B, and a chemoselective and stereoselective oxidation with Murray's reagent to install the requisite C-10b hydroxyl group in 9-deoxy-PF1233s A-B. The present synthesis also established the absolute configuration of javanicunine B.