The international harbors and fishing ports in Taiwan are nearly not installed the wastewater or oil treatment facilities, which would cause the ocean pollution by the ballast and bilge water from the boats. The purpose of this research is to study the feasibility of treatment of diesel fuel and the polycyclic aromatic hydrocarbons (PAHs) in diesel by aerobic biofiltreation in salty environment. According to the experimental results, the mineral oil and PAHs in the diesel fuel present high good removal efficiencies. Both of the contaminants were decomposed fast at the first 8 hours, and then slow down. The emulsified diesel fuel were found able to be reduced 83% within 8 hours, and the concentrations of phenanthrene would found decreased from 1.5 to 0.1 mg/L. After 8 hours, we observed that the PAHs with high number of rings kept a mild diminish trend, while the PAHs with less rings exhibited arrearage and irregular indicated by some peaks appearing in the chromatography diagram of HPLC, which were not found in the diagram in the initial of test run. In conclusion, the aerobic biofiltreation systems were found able to degrade n-alkanes and PAHs in diesel fuel effectively. Thus we suggested to install the systems at the greasiness accepting facilities in the harbor. However, we still have to keep studying the influence of the interrelationship between the contaminants in diesel fuel and the environment factors.