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[1] The Mediterranean and Black Seas are unique marine environments subject to important anthropogenic pressures due to atmospheric and riverine inputs of organic pollutants. They include regions of different physical and trophic characteristics, which allow the studying of the controls on pollutant occurrence and fate under different conditions in terms of particles, plankton biomass, interactions with the atmosphere, biodegradation, and their dependence on the pollutant physical chemical properties. Polycyclic Aromatic Hydrocarbons (PAHs) have been measured in samples of seawater (dissolved and particulate phases) and plankton during two east-west sampling cruises in June 2006 and May 2007. The concentrations of dissolved PAHs were higher in the south-western Black Sea and Eastern Mediterranean than in the Western Mediterranean, reflecting different pollutant loads, trophic conditions and cycling. Particle and plankton phase PAH concentrations were higher when lower concentrations of suspended particles and biomass occurred, with apparent differences due to the PAH physical chemical properties. The surface PAH particle phase concentrations decreased when the total suspended particles (TSP) increased for the higher molecular weight (MW) compounds, consistent with controls due to particle settling depletion of water column compounds and dilution. Conversely, PAH concentrations in plankton decreased at higher biomass only for the low MW PAHs, suggesting that biodegradative processes in the water column are a major driver of their occurrence in the photic zone. The results presented here are the most extensive data set available for the Mediterranean Sea and provide clear evidence of the important physical and biological controls on PAH occurrence and cycling in oceanic regions.