Abstract. Surface sediments collected from deep basins (22 stations, 1018–4087 m depth) of the Eastern Mediterranean Sea (EMS) were analyzed for aliphatic, triterpenoid and polycyclic aromatic hydrocarbons (PAHs) as tracers of natural and anthropogenic inputs. Concentrations of total aliphatic hydrocarbons (TAHC), n-alkanes (NA) and the Unresolved Complex Mixture (UCM) of aliphatic hydrocarbons ranged 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 total PAHs (TPAH25) concentrations ranged from 11.6 to 223 ng g?1. Molecular profiles of aliphatic hydrocarbons and PAHs reflect the contribution of both natural (epicuticular plant waxes) and anthropogenic (degraded petroleum products, unburned fossil fuels and combustion of petroleum, grass, wood and coal) compounds in deep EMS sediments, with hydrocarbon mixtures displaying significant regional variability. Hydrocarbon concentrations correlated significantly with the Total Organic Carbon (TOC) content of sediments, indicating that organic carbon exerts an important control on their transport and fate in the study area, while strong sub-basin and mesoscale variability of water masses also impact their regional characteristics. Major findings of this study support that deep basins/canyons of the EMS could act as traps of both natural and anthropogenic hydrocarbons.