An efficient stereoselective synthesis of the C14–C29 fragment highlighting a coupling reaction between a 1,3-dithiane derivative and an α-branched aldehyde was realized. This highly convergent synthesis involved two chiral pools, L-malic acid and (+)-camphorsulfonic acid, which are the starting compounds to control the six stereogenic centers present in the C14–C29 fragment of amphidinol 3.