Worldwide, shipyards/manufacturers of cruise and roll-on/roll-off vessels have adopted steel-aluminium joints made by explosion welding to join steel plates of the hull to aluminium plates of the decks. This work illustrates that the environment friendly welding technology friction stir welding (FSW) has great potential for application in the shipbuilding industry. The effect of the welding process parameters on the joining of the dissimilar materials AA6082 and AISI316 has been investigated. It is shown that the tool offset is one of the most important process parameters for these kind of dissimilar joints. Mechanical properties for dissimilar aluminium to steel joints with ultimate tensile strength above 200 MPa have been reached, where the joints showed ductile failure. Overall, FSW can be a suitable option to substitute current technologies, such as explosion welding, due to its simple set up, low CO2 emission and high manufacturing safety.