Abstract. Surface sediments collected from deep basins (1018–4087 m depth) of the eastern Mediterranean Sea (Ionian Sea, southern Aegean Sea and northwestern Levantine Sea) were analyzed for aliphatic and polycyclic aromatic hydrocarbons as tracers of natural and anthropogenic inputs. Concentrations of total aliphatic hydrocarbons, n-alkanes and the unresolved complex mixture (UCM) of aliphatic hydrocarbons varied significantly, ranging from 1.34 to 49.2 μg g−1, 145 to 4810 ng g−1 and 0.73 to 36.7 μg g−1, respectively, while concentrations of total polycyclic aromatic hydrocarbons (PAHs) ranged between 11.6 and 223 ng g−1. Molecular profiles of determined hydrocarbons reflect a mixed contribution from both natural and anthropogenic sources in deep-sea sediments of the eastern Mediterranean Sea, i.e., terrestrial plant waxes, degraded petroleum products, unburned fossil fuels and combustion of grass, wood and coal. Hydrocarbon mixtures display significant variability amongst sub-regions, reflecting differences in the relative importance of inputs from various sources and phase associations/transport pathways of individual hydrocarbons that impact on their overall distribution and fate. Hydrocarbon concentrations correlated significantly with the organic carbon content of sediments, indicating that the latter exerts an important control on their transport and ultimate accumulation in deep basins. Additionally, water masses' circulation characteristics also seem to influence the regional features and distribution patterns of hydrocarbons. Our findings highlight the role of deep basins/canyons as repositories of both natural and anthropogenic chemical species.