Deep-sea ecosystems play a key role in the cycling and vertical transfer of matter and energy in oceans. Although the contamination of deep-sea demersal and benthic organisms by persistent organic pollutants has been proven, deep pelagic species have been far less studied. To fill these gaps, we studied the occurrence of a large variety of hydrophobic organic contaminants including polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), legacy and alternative brominated flame retardants (BFRs) and per- and polyfluoroalkyl substances (PFASs) in crustaceans and fish species collected in the Bay of Biscay, northeast Atlantic. The results highlighted the global predominance of PCBs in fish, followed by OCPs, PFASs and PBDEs, with highly variable concentrations among species. Most of the chlorinated or brominated contaminants showed increasing concentrations with increasing δ15N values, while most PFASs showed inverse trends. The contaminant profiles and diagnostic ratios revealed species-specific metabolic capacities and peculiar contribution of highly-brominated BFRs.