Different ships use different fuels according to their needs. Most large cargo ships use bunker fuel which is a form of crude oil. Some ships use diesel fuel. Some modern commercial ships are employing nuclear fuels. Some military ships use diesel for their normal operating engines and for more speed they will use jet fuel for gas turbine engines.
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The most common fuel used is Bunker C / #6 fuel oil because of it's cheapness. However, it is not as good for the environment as Marine Diesel. Marine Diesel is also several times more expensive. This is why it in not used in ships.
Most modern cargo ships will use Heavy Fuel Oil, otherwise known as bunker fuel.
Some ships will have a tanks of diesel fuel (Marine Gas Oil) for use in either their main engine or electrical generators.
It depends on the ship.
Coal, bunker oil, diesel, jet fuel, and in the case of nuclear power uranium is used. There are even a lot of sailing ships in use throughout the world.