Accurate interpretation of mercury (Hg) isotopic data requires the consideration of several biotic factors such as age, diet, geographical range, and tissue metabolic turnover. A priori knowledge of prey-predator isotopic incorporation rates and Hg biomagnification is essential. This study aims to assess Hg stable isotopes incorporation in an Arctic species of Phocidae, the hooded seal Cystophora cristata, kept in human care for 24 months (2012–2014) and fed on a constant diet of Norwegian Spring Spawning herring Clupea harengus. We measured THg, MMHg and iHg levels, as well as Hg stable isotope composition with both mass dependent (MDF) and mass independent (MIF) fractionation (e.g. δ202Hg and Δ199,200,201,204Hg) in hooded seal kidney, liver, hair and muscle, in addition to herring muscle. We then calculated Hg MDF and MIF isotopic fractionation between hooded seals and their prey. We found a significant shift in δ202Hg between hooded seal hair (+0.80‰) and kidney (−0.78‰), and herring muscle. In hooded seals tissues δ202Hg correlated positively with MMHg percentage. These findings suggest that tissue-specific Hg speciation is the major driver of changes in Hg isotopic fractionation rates in this Arctic predator. Δ199Hg, Δ200Hg, Δ201Hg and Δ204Hg values did not vary between herring and hooded seal tissues, confirming their utility as tracers of Hg marine and atmospheric sources in top predators. To our knowledge, this represents the first attempt to assess complex Hg isotope dynamics in the internal system of Arctic Phocidae, controlling the effects of age, diet, and distribution. Our results confirm the validity of Hg stable isotopes as tracers of environmental Hg sources even in top predators, but emphasize the importance of animal age and tissue selection for inter-study and inter-species comparisons