The food and feeding ecology of the poorly known southern long-finned pilot whale (Globicephala melas edwardii) was investigated using ecological tracers (muscle and skin δ13C and δ15N, and total mercury, Hg) on individuals from two mass strandings together with at-sea observations of live animals in Kerguelen waters, southern Indian Ocean. Sightings of cetaceans from long-liners over 9 years (2003–2012) emphasized the regular occurrence of pilot whales in slope waters surrounding the archipelago. Tissue δ13C values (a proxy of consumer foraging habitat) suggest that pilot whales fed in slope waters and in oceanic subantarctic waters over the last months preceding stranding. Tissue δ15N values and Hg concentration (dietary proxies) indicate a high trophic position (~4.7) for the pilot whales, likely corresponding to a mixed diet of fish and squid (not crustaceans) of undetermined species. Both skin and muscle Hg concentrations were positively and linearly correlated to individual size with no concomitant δ15N changes, which can be interpreted as a progressive Hg accumulation in tissues of individuals throughout life with no parallel dietary shift. Skin and muscle Hg concentrations were linearly and positively related; hence, Hg skin could be used as a proxy of Hg concentration in muscle (a main Hg reservoir of the body). Kerguelen southern long-finned pilot whales were less Hg contaminated than most pilot whale populations studied so far, thus suggesting that they are not at a high risk to Hg-induced damages in the remote islands of the Southern Ocean.