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Many ships are switching to low sulfur fuel oil due to the global sulfur cap 2020. The switch to low sulfur fuel oil is expected to reduce not only SOx but also organic pollutants contained in PM. In this study, the emission characteristic of polycyclic aromatic hydrocarbons (PAHs), a type of organic pollutants contained in PM, was evaluated before and after the global sulfur cap 2020, by collecting PM emitted from a ship in operation. Among PAHs, the 27 compounds that have been drawing attention due to their impact on living organisms were measured. The main engine of the ship was a two-stroke marine diesel engine, and the ship was operated by using alternatively heavy fuel oil and low sulfur fuel oil (LSA oil). The engine load was increased stepwise from 25%, 50%, 75%, to 90%, and PM was collected at each load. As a result, the total emission of the 27 compounds was decreased due to switching to LSA oil, then the impact on the atmospheric environment was reduced. While, the 2 compounds, Pyrene and Benzo[a]anthracene, emission was increased. Lastly, the emission concentration of the 27 compounds decreased proportionately to the rise of the engine load for both cases using heavy fuel oil and LSA oil, while, there was also the part unique to a ship in operation.