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These data relate to the research article entitled “Imprint and short-term fate of the Agia Zoni II tanker oil spill on the marine ecosystem of Saronikos Gulf” by Parinos et al., 2019 [1]. The dataset includes the concentrations of 32 individual compounds/groups of polycyclic aromatic hydrocarbons (PAHs) determined in 235 seawater samples and 55 sediment samples analyzed during the monitoring survey conducted by the Hellenic Centre for Marine Research (H.C.M.R.) following the September 2017 Agia Zoni II heavy fuel oil (HFO) spill incident in Saronikos Gulf, Greece. The survey effort included 69 seawater sampling sites, of which 55 coastal and 14 open sea areas, and 22 sediment sampling sites across the inner Saronikos Gulf, aiming to assess the spatial and temporal imprint of the spilled oil during the first six months from the incident. The data were acquired by means of gas chromatography - mass spectrometry, following proper pre-treatment of the collected samples. This dataset is, to the best of our knowledge, the very first PAHs record related to the Agia Zoni II oil spill incident, that should be of interest for future scientific research on this and HFO spills in general. Keywords: Polycyclic aromatic hydrocarbons, Heavy fuel oil, Group IFO 380, Oil pollution