There are conflicting findings over the bioavailability of long-chain n-3 polyunsaturated fatty acids (n-3 PUFA) from krill oil (KO) compared with fish oil (FO) in short- and long-term studies. The aim of this study was to compare the effects of KO versus FO on the enrichment of molecular species of plasma phospholipids in young women following a 30-day consumption of the n-3 oils. Eleven healthy women aged 18–45 years consumed seven capsules of KO per day (containing a total of 1.27 g n-3 PUFA) or five capsules of FO per day (total of 1.44 g n-3 PUFA) for 30 days in a randomized crossover study, separated by at least a 30-day washout period. Fasting blood samples were collected at day zero (baseline), day 15 and day 30 and analyzed by HPLC-MS/MS for molecular species of phospholipids. Supplementation increased n-3 PUFA in main phospholipids classes in both groups. After 30 days of supplementation, 35 out of 70 molecular species containing eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and docosapentaenoic acid (DPAn-3) had a significantly greater concentration in KO group compared with the FO treated group. The majority (89%) of the differentiated molecular species were choline and ethanolamine ether-phospholipids. These data reveal that analysis of plasma phospholipids following 30 days of consumption of KO (a marine oil rich in phospholipids, including ether phospholipids) resulted in an enrichment of n-3 PUFA in molecular species of ether-phospholipids compared with FO (a triacylglycerol-rich marine oil).