Since mercury (Hg) biogeochemistry in the Southern Ocean is minimally documented, we investigated Hg stable isotopes in the blood of seabirds breeding at different latitudes in the Antarctic, subantarctic and subtropical zones. Hg isotopic composition was determined in adult penguins (5 species) and skua chicks (2 species) from the Adélie Land (66°39′S, Antarctic) to Crozet Islands (46°25′S, subantarctic) and Amsterdam Island (37°47'S, subtropical). Mass-dependent (MDF, δ202Hg) and mass-independent (MIF, ∆199Hg) Hg isotopic values separated populations geographically. Antarctic seabirds exhibited lower δ202Hg values (-0.02 to 0.79 ‰, min-max) than subantarctic (0.88 to 2.12 ‰) and subtropical (1.44 to 2.37 ‰) seabirds. In contrast, ∆199Hg values varied slightly from Antarctic (1.31 to 1.73 ‰) to subtropical (1.69 to 2.04 ‰) waters. The extent of methylmercury (MeHg) photodemethylation extrapolated from ∆199Hg values was not significantly different between locations, implying that most of the bioaccumulated MeHg was of mesopelagic origin. The larger increase of MDF between the three latitudes co-varies with MeHg concentrations. This supports an increasing effect of specific biogenic Hg pathways from Antarctic to subtropical waters, such as Hg biological transformations and accumulations. This “biogenic effect” among different productive southern oceanic regions can also be related to different mixed layer depth dynamics and biological turnover that specifically influence the vertical transport between the mesopelagic and the photic zones. This study shows the first Hg isotopic data of the Southern Ocean at large scale and reveals how regional Southern Ocean dynamics and productivity control marine MeHg biogeochemistry and the exposure of seabirds to Hg contamination.