The southern elephant seal (SES; Mirounga leonina ) has a circumpolar distribution, breeding mainly on sub‐Antarctic islands and making long trips between breeding or molting and foraging areas. Most individuals from colonies in the South Shetland Islands (western Antarctic Peninsula; WAP) are distributed in Antarctic Specially Protected Areas (ASPA). Despite these protected habitats, pollutants can reach such remote areas far away from emission sources, affecting local fauna. To assess possible mercury (Hg) contamination in SES, we analyzed skin samples collected from free‐ranging molting individuals using the remote biopsy PAXARMS system in Isla 25 de Mayo/King George Island (62°15′S, 58°39′W; ASPA 132). Hairless skin samples were analyzed to determine total‐Hg (THg) concentrations, which ranged between 145 ng/g and 1,915 ng/g ( M = 730, SD = 388 ng/g), showing significant differences between sexes, with adult‐females having higher concentrations (range = 306–1,915, M = 859, SD = 427 ng/g dw) than subadult‐males (range = 145–1,645, M = 629, SD = 329 ng/g dw). These differences may be explained mainly by feeding‐niche partitioning between sexes. Females prefer mesopelagic prey or prey associated with sea‐ice in the WAP, which are enriched in methylmercury. These results provide insight regarding Hg contamination in top Antarctic predators like SES, and the need to monitor for potential effects of Hg contamination in Antarctic marine mammals.