The objectives of this study were to explore trophic levels and possible diet overlap between harp seals (Pagophilus groenlandicus) and common minke whales (Balaenoptera acutoroostrata) in the Barents Sea using stable isotopes of nitrogen (δ15N) and carbon (δ13C) and fatty acid analyses, and to explore the energy pathways from the plankton to the top predators. Blubber and muscle samples from 93 harp seals and 20 minke whales were collected in the southern Barents Sea in May 2011. The study showed that harp seals were at a higher trophic level than minke whales during spring. This supported previous diet studies suggesting a more fish-dominant diet for seals, as compared with the whales, at this time of the year. The stable isotopes and fatty acids indicated niche separation between the seals and the whales, and between different age groups of the harp seals. Older seals had fatty acid profiles more equal to minke whales as compared with younger seals. Furthermore, while the fatty acid profiles suggested that krill were of particular importance for the young seals, the profiles from older seals and whales suggested that fish dominated their diets.