The climate change-induced northward movement of sub-Arctic marine mammals increases their range overlap and interactions with native Arctic species. We compared feeding patterns of 11 marine mammal species (4 Arctic and 7 sub-Arctic) in Greenland using stable isotope ratios and fatty acid signatures, and also assessed the effects of lipid extraction on stable isotope ratios. Lipid extraction showed limited increases in δ13C, intermediate effects on δ15N, and significant depletion of δ34S in muscle of some marine mammals. Arctic and sub-Arctic species differed in stable isotope ratios, indicating some use of separate food resources, while likely also reflecting baseline isotopic variation. Proportions of some of the most abundant fatty acids (20:1n9, 22:1n11, 20:5n3, 22:6n3) varied between Arctic and sub-Arctic species, indicating that sub-Arctic species rely mostly on a pelagic food web, while Arctic species exploit an ice-associated and benthic food web, although the sub-Arctic harp and hooded seals and Arctic narwhal showed opposite patterns. Sub-Arctic species had the largest niche breadths, implying diet flexibility and potential to adapt to further changes. Overall patterns in dietary tracers demonstrate separation of feeding niches between most Arctic and sub-Arctic marine mammals, but potential niche overlap and shared food resources for some species. Sub-Arctic seal species overlap the feeding niches of native Arctic species the most of all range-shifters, and of Arctic species, narwhal appear to be the most vulnerable to niche overlap and potential food competition with northward-shifting species.