The non-essential metal mercury (Hg) can have deleterious effects on health of organisms, and tends to bioaccumulate with age in long-lived organisms and to biomagnify along food chains. Because sharks are fished for human consumption and their Hg levels are frequently above the maximum Hg concentration recommended for fish consumption, understanding the drivers of Hg concentration is of considerable interest. Total Hg concentrations were analysed in muscle tissues of 14 shark and 2 batoid species (n = 339 individuals) sampled across multiple habitats (coastal, oceanic and bathyal) in the southwestern Indian Ocean. Stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) were analysed to assess whether relative trophic position and foraging habitats affected Hg concentrations. Hg concentrations increased with δ15N and body length, highlighting the mechanisms of bioaccumulation and biomagnification in relation with the trophic position and size of the individuals. Habitats where elasmobranchs were collected also affected their Hg concentrations. Bathyal sharks had high Hg concentrations that were almost similar to those of oceanic species, despite their lower relative trophic position. Higher bioavailability of Hg due to its enhanced methylation in deeper waters was considered as the most likely explanation for this result. These results highlight that multiple factors contribute to mercury accumulation in elasmobranchs.