- In an attempt to elucidate the biosynthesis of the polyunsaturated fatty acid eicosapentaenoic acid (20:5ω3, EPA), we treated cultures of the eustigmatophyte Monodus subterraneus Peterson with either salicylhydroxamic acid or the herbicide SAN 9785. Labeled linoleic acid was incorporated into the cultures in the presence and absence of the latter inhibitor, and the redistribution of label was followed. Our results suggest that the major biosynthetic pathway leading to EPA involves fatty acids of the ω6 family. In the early stages of the biosynthesis, 18:1 is predominantly incorporated to the sn‐2 position of phosphatidylcholine, where it is stepwise desaturated by the Δ12 and Δ6 desaturases to 18:3ω6. The latter is released from the lipid, elongated to 20:3ω6 and reincorporated to both positions of phosphatidylethanolamine (PE) where it is further desaturated by the Δ5 and ω3 desaturases to EPA. We suggest that PE is the donor of the 20:5/20:5 diacylglycerol that is imported to the chloroplast to form the eukaryotic‐like molecular species of monogalactosyldiacylglycerol. Likewise, 20:3ω6 can be also incorporated into diacylglyceryltrimethylhomoserine, mostly to the sn‐2 position and similarly desaturated to 20:4ω6 and 20:5ω3. These fatty acids can be exported and incorporated into the sn‐1 position of the prokaryotic‐like molecular species of the chloroplastic lipids. We thus suggest that both the eukaryotic‐like and the prokaryotic‐like molecular species are biosynthesized by different extraplastidial lipids.