Krill oil is currently among the most highly promoted products in the dietary supplement market, which, due to its high price, can be potentially adulterated with fish species and artificial oil. For a holistic control of krill oil quality, ¹H, ¹³C, and ³¹P nuclear magnetic resonance (NMR) spectroscopies were used. The fatty acid and phospholipid composition as well as secondary ingredients, such as homarine, amino acids, and chitin, were examined. The following phospholipid species were detected: phosphatidylcholine (75–85 mol %), phosphatidylethanolamine (4–7 mol%) and their lyso derivatives 1-lysophosphatidylcholine (1–2 mol%)–2-lysophosphatidylcholine (10–16 mol%) and lysophosphatidylethanolamine (1 mol%). In the -2 position of phospholipids, the content of eicosapentaenoic acid (mean 68.23%; relative standard deviation 2.23%) was twice as high as the content of docosahexaenoic acid (mean 31.77%; relative standard deviation 4.79%). ¹³C NMR spectroscopy was used to distinguish between krill and fish oil-based dietary supplements. The adulteration of krill oil can be detected by fatty acid distribution in the sn-2 triacylglycerol position. The sensitivity of the method is about 10% (w/w) of fish content in blends, which is enough to detect deliberate adulteration. The same methodology can be used to recognize synthetically modified krill oil. The method was successfully applied to 30 commercially available krill and fish oil supplements.