Diesel soot particles were sampled from 2-stroke and 4-stroke engines that burned two different fuels (Bunker A and C, respectively), and the effects of the engine and fuel types on the structural characteristics of the soot particle were analyzed. The carbon nanostructures of the sampled particles were characterized using various techniques. The results showed that the soot sample collected from the 4-stroke engine, which burned Bunker C, has a higher degree of order of the carbon nanostructure than the sample collected from the 2-stroke engine, which burned Bunker A. Furthermore, the difference in the exhaust gas temperatures originating from the different engine and fuel types can affect the nanostructure of the soot emitted from marine diesel engines.