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International audience; Long-chain polyunsaturated fatty acids (LC-PUFA) are molecules produced at the basis of marine food webs and essential for ecosystem functioning. This study reports detailed fatty acid (FA) composition including the two LC-PUFA 20:5n-3 and 22:6n-3, in suspended organic matter (SPOM) from the upper 300 m collected in the Kerguelen Island region in the Southern Ocean during the post-bloom period (February–March 2018; project MOBYDICK). FA profiles were largely dominated by PUFA (53–69% of Total Fatty Acid, TFA) regardless of stations and among PUFA, proportions of LC-PUFA were especially high, making up 27–44% of TFA both in the ML and upper mesopelagic. 20:5n-3 and 22:6n-3 co-occurred in the ML as a result of the post-bloom phytoplankton community showing a mixed composition dominated by small size phytoplankton (prymnesiophytes and prasinophytes) supplying 22:6n-3, and with diatoms in lower proportions supplying 20:5n-3. Elevated levels of LC-PUFA were observed both inside the iron-fertilized area on the Kerguelen Plateau and downstream, and outside in High Nutrient Low Chlorophyll waters located upstream of the Plateau, and appeared unrelated to site. In the upper mesopelagic, both LC-PUFA were maintained at high relative proportions suggesting an efficient and possibly fast vertical transfer from the surface. Transfer with depth seems to proceed via distinct pathways according to LC-PUFA. 20:5n-3 may be exported along with diatoms, presumably in the form of large intact cells, aggregates as well as resting spores. For 22:6n-3, transfer may involve a channeling through the heterotrophic food web resulting in its association with fecal material at depth. Channeling of 22:6n-3 could involve heterotrophic protists such as dinoflagellates and ciliates grazing on small phytoplankton, as well as larger zooplankton such as copepods and salps, possibly feeding on microzooplankton and producing fecal pellets rich in 22:6n-3. According to LC-PUFA content, SPOM present throughout the upper water column (0–300 m) appeared of high nutritional quality both on- and off-plateau, and represented a valuable source of food for secondary consumers and suspension feeders.