There are so many difficulties of melt bonding mainly applied for hull construction of a aluminum alloy small boat. For resolving this problem, Friction stir welding(FSW) in non-melting solid state welding Process generally is applied in the transport industry. This paper is studied the joining strength characteristics and macrostructure according to dissimilar aluminium 5000/6000 alloy joining for a small boat applied for this FSW technology. It is reported that difference of joining strength in accordance with the direction of rotation in case of friction stir welding between dissimilar metals(Al/Cu, Al/Fe) is also highly large. In this study, Test is carried out by making the specimen according to the direction of rotation of dissimilar aluminium alloy joining.