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This distribution and variation of 45 polycyclic aromatic hydrocarbons (PAHs) in the waters of Kenting coral reefs were investigated by using sensitive research-grade sampling and analytical methods. The concentration levels of total PAHs (including particulate and dissolved PAHs) in the Kenting waters were relatively low, ranging from 2.2 to 34.4 ng/L. There was no significant spatial difference in PAH concentrations among the sampling stations, even between the surface and bottom waters. The fraction of dissolved PAHs on average was greater than that of particulate PAHs due to the small amount of total suspended particles. The partition coefficients between the particulate and dissolved phase (log K(oc)) were positively correlated with their log K(ow) values (r(2) = 0.67, n = 80), except for the more hydrophobic PAHs with log K(ow) values greater than 5.91. Results of principal component analysis indicate that the patterns of particulate PAH compositions were similar through the Kenting waters in the fall and winter, whereas there was a significant spatial difference between the spring and summer samples, which might be affected by a combination of land runoff and coastal currents. PAHs along the Kenting coasts were dominated by low-molecular PAHs, which have higher solubility than high-molecular PAHs. Based on isomer ratios, analysis of the source of PAHs in the Kenting coastal waters demonstrated that the PAHs come mostly from petroleum and, to a lesser degree, from combustion.