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Fatty acid analysis is a powerful tool in food web research for estimating dietary sources in marine predators. However, the utility of fatty acids as dietary indicators from whole lipid samples, rather than from separate lipid classes, has been questioned. Samples are often collected at a single time point, precluding seasonal dietary comparisons. We investigated variations in the fatty acid composition of structural (phospholipids) and storage lipids (triacylglycerols) of Antarctic krill (Euphausia superba) using fisheries samples obtained over one year. Seasonal variation was observed in fatty acid biomarkers within triacylglycerol and phospholipid fractions of krill. Fatty acids in krill triacylglycerols (thought to better represent recent diet), reflected omnivorous feeding with highest percentages of flagellate biomarkers (18:4n-3) in summer, and diatom biomarkers (16:1n-7c) in autumn, winter and spring. Carnivory biomarkers (∑ 20:1 + 22:1 and 18:1n-9c/18:1n-7c) in krill were greater in autumn. Phospholipid fatty acids were less variable and higher in 20:5n-3 and 22:6n-3, which are essential components of cell membranes. Sterol composition did not yield detailed dietary information, but percentages of the major krill sterol, cholesterol, were significantly higher in winter and spring compared with summer and autumn. Unexpectedly, 18:4n-3 and copepod markers ∑ 20:1 + 22:1 were not strongly associated with the triacylglycerol fraction during some seasons. Krill may mobilise 18:4n-3 to phospholipids for conversion to long chain polyunsaturated fatty acids, which would have implications for its role as a dietary biomarker. For the first time, we demonstrate the dynamic seasonal relationship between specific biomarkers and krill lipid classes.