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Distribution, sources, and ecological risk of 43 compounds of polycyclic aromatic hydrocarbons (PAHs) in surficial sediments of the Persian Gulf were investigated. The sediments were sampled from 60 offshore stations during an oceanographic cruise in the winter of 2012. Gas chromatography high-resolution mass spectrometry was used for the PAHs determinations in sediment samples. The concentrations of 21 parent PAHs, 7 methylated PAHs, 11 oxygenated PAHs and 4 nitrated PAHs were 9.0–201.5 ng g−1 dw, 3.3–60.3 ng g−1 dw, 15.2–172.7 ng g−1 dw and 0.1–8.3 ng g−1 dw, respectively. Among 21 parental PAHs, naphthalene (29.35 ng g−1 dw), phenanthrene (4.6 ng g−1 dw), and pyrene (3.18 ng g−1 dw) were the most abundant compound. 1-acenaphthenone (43.41 ng g−1 dw) and 2-methylnaphthalene (7.15 ng g−1 dw) showed the highest concentration in the oxy- and methyl-PAHs, respectively. The concentrations of nitro-PAHs were between not detected to 4 ng g−1 dw. According to the ecological risk assessment, the calculated total toxicity of PAHs was at below the lethal level on benthic organisms in all stations in the Persian Gulf, but there is risk of toxicity for the benthic organism in the Gulf of Oman (from the Strait of Hormuz to Jask). In general, nitrogenated and oxygenated derivatives did not show a significant risk in the study area. Based on the diagnostic ratios, the mixed sources (both petrogenic and pyrogenic) and pyrogenic sources have been identified for PAHs. Biomass combustion source has been identified for the stations near flares and gas fields. Principle component analysis-multivariate linear regression analysis for source identification shows that maritime traffic, abundant flares that burn the gas in oil, gas fields and dust storms have a major impact on the production of PAHs in this area.