The biochemical composition of Antarctic krill, Euphausia superba, is largely determined by their feeding behaviour. As they supply energy for animals of a higher trophic level and are also commercialized for human consumption, the interest in research on the species is high. Lipids, especially phospholipids, make up a high proportion of dry weight in krill. Seasonal changes are well documented in the fingerprint of free fatty acids analysed after hydrolysis of phospholipids, but the underlying intact polar lipids are rarely considered. In this study, we evaluated the compositions of intact phospholipids (IPLs) in the stomach, digestive gland and hind gut of Antarctic krill caught in summer and autumn at the Antarctic Peninsula region. Using high-resolution mass spectrometry, the fatty acid composition of 179 intact phospholipids could be resolved. Most IPLs were phosphatidylcholines, followed by phosphatidylethanolamines. Several very long chain polyunsaturated fatty acids up to 38:8, which have not been reported in krill before, were identified. The composition shifted to higher molecular weight IPLs with a higher degree of unsaturation for summer samples, especially for samples of the digestive gland. The data supplied in this paper provides new insights into lipid dynamics between summer and autumn usually described by free fatty acid biomarkers.