The chemical composition of particulate matter (PM) emissions from a medium-speed four-stroke marine engine, operated on both heavy fuel oil (HFO) and distillate fuel (DF), was studied under various operating conditions. PM emission factors for organic matter, elemental carbon (soot), inorganic species and a variety of organic compounds were determined. In addition, the molecular composition of aromatic organic matter was analyzed using a novel coupling of a thermal-optical carbon analyzer with a resonance-enhanced multiphoton ionization (REMPI) mass spectrometer. The polycyclic aromatic hydrocarbons (PAHs) were predominantly present in an alkylated form, and the composition of the aromatic organic matter in emissions clearly resembled that of fuel. The emissions of species known to be hazardous to health (PAH, Oxy-PAH, N-PAH, transition metals) were significantly higher from HFO than from DF operation, at all engine loads. In contrast, DF usage generated higher elemental carbon emissions than HFO at typical load points (50% and 75%) for marine operation. Thus, according to this study, the sulfur emission regulations that force the usage of low-sulfur distillate fuels will also substantially decrease the emissions of currently unregulated hazardous species. However, the emissions of soot may even increase if the fuel injection system is optimized for HFO operation.