Despite their remoteness, deep-sea species bioaccumulate mercury, mostly in the form of the neurotoxin methylmercury (MeHg). Although the concentration of MeHg in the water column is known to increase with depth down to a maximum found at the base of the permanent thermocline, the knowledge of the relationship between MeHg content in marine species and their depth of occurrence is limited. We analyzed total mercury (THg) and MeHg concentrations in 25 species of fish inhabiting the Avilés Submarine Canyon and its adjacent shelf (Cantabrian Sea, North-East Atlantic) between 50 and 1868 m depth. THg concentrations ranged from 0.03 μg g−1 in wet weight (ww) in Chauliodus sloani and 4.0 μg g−1 ww in Coryphaenoides guentheri. 65% of the species analyzed exceeded 0.5 μg g−1 ww of MeHg, the maximum level for safe consumption recommended by FAO/WHO. THg and MeHg contents in muscle tissue increased with the depth of occurrence of fish and was influenced by their habitat so that demersal species had higher THg content than pelagic species inhabiting the same depth. MeHg accounted for an average 76 ± 3.9% of THg (mean ± SD), which is lower than that reported for other fish communities and can be explained by the high concentration of Hg present in sediments of the Nalón estuary, which discharges right off the Avilés Canyon head. The % of THg as MeHg was also strongly correlated with δ15N values, confirming that MeHg can be an indicator of the trophic identity of a species within the food web.