Analysis of the 16 polycyclic aromatic hydrocarbons (PAHs) of the US Environmental Protection Agency priority pollutant list was carried out in sediment samples of an industrial port in the southern Kaohsiung Harbor of Taiwan which is supposed to be extensively polluted by industrial wastewater discharges. The determination and quantification of PAHs in sediment samples were performed using gas chromatography coupled to mass spectrometry (GC-MS) with the aid of deuterated PAH internal standards and surrogate standards. The total concentrations of the 16 PAHs varied from 4,425 to 51,261 ng/g dw, with a mean concentration of 13,196 ng/g dw. The PAHs concentration is relatively high in the river mouth region, and gradually diminishes toward the harbor region. Diagnostic ratios showed that the possible source of PAHs in the industrial port area could be coal combustion. As compared with the US Sediment Quality Guidelines (SQGs), the various observed levels of PAHs exceeded the effects range median (ERM), and could thus cause acute biological damages. The results can be used for regular monitoring, and future pollution prevention and management should target the various industries in this region for reducing pollution.