Knowledge of the trophic ecology of zooplankton is essential for evaluating their functional roles in marine food webs and nutrient cycling since they represent the link between primary producers and higher trophic levels. Here we investigated the fatty acid (FA) composition of different zooplankton size classes and selected species collected at the vicinity of the Sub-Antarctic Kerguelen Islands in late austral summer 2018 as part of the MOBYDICK research project. The analysis revealed that zooplankton FA composition varied significantly across size classes and species but not among stations. Larger zooplankton generally had higher total FA (TFA) amounts per dry weight (22.1 ± 3.0 vs. 61.9 ± 11.8 mg g-1). Essential FAs (EFA) accounted for 40.5 ± 0.8 % of TFA, with 22:6n-3 (DHA) and 20:5n-3 (EPA) being the most prominent. Diatom trophic markers (TM) were abundant in larger zooplankton size classes, while non-diatom TM were more prevalent in smaller size classes. The FA-based nutritional quality index (NQI) of zooplankton was positively correlated with EFA and DHA, and it was higher than the NQI of phytoplankton concurrently collected, indicating its better nutritional quality compared to primary producers. This study highlights the importance of size and species-specific dietary preferences in determining zooplankton FA profiles and the high nutritional quality of this group collected during late austral summer, which significantly contribute to our understanding of zooplankton's ecological role in marine food webs in the Southern Ocean.