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Polycyclic aromatic hydrocarbons (PAHs) are toxic and ubiquitous in the environment and pose great risks. Bioaccumulation by plankton is the outset for PAHs entering marine food web. The long-term driving environmental factors for bioaccumulation of PAHs in zooplankton have not been well investigated. In this study, high variation of PAH concentrations in zooplankton (5 to 5440 ng g(-1) dry weight) was found, with the highest PAH levels near the transect Kaohsiung Harbor. Precipitation significantly enhances the PAH concentration in zooplankton and affects the PAH distribution in the water column, indicating PAH input from terrestrial runoff. The sources of PAHs in the coastal waters are a mixture of petroleum and combustion. Biomass dilution dominates bioaccumulation of PAHs in zooplankton, especially for the dominant species, copepods. This study provides the first information on PAH bioaccumulation in zooplankton to understand PAH transport in the plankton food web in subtropical coastal waters.