Deep-pelagic species are central to marine ecosystems and increasingly vulnerable to global change and human exploitation. To date, our understanding of these communities remains limited mainly due to the difficulty of observations, calling for complementary innovative tools to better characterize their ecology. We used mercury (Δ199Hg, δ202Hg, Δ201Hg, and Δ200Hg), carbon (δ13C), and nitrogen (δ15N) stable isotope compositions to segregate deep-pelagic species caught on the continental slope of the Bay of Biscay (NE Atlantic) according to their foraging depth and trophic ecology. Decreasing fish Δ199Hg values with corresponding depth estimates from the surface to down to 1,800 m confirmed that mercury isotopes are able to segregate deep species over a large vertical gradient according to their foraging depth. Results from isotopic compositions also identified different mercury sources, likely reflecting different trophic assemblages over the continental slope, in particular, the demersal influence for some species, compared to purely oceanic species. Overall, our results demonstrate how mercury stable isotopes can inform the vertical foraging habitat of little-known species and communities feeding in the deep.