Abstract: Dissimilar 5083/6082 Al alloys friction stir welding (FSW) joint was experimentally investigated. Effects of the shoulder diameter on the cross section morphology, microstructure and microhardness are mainly discussed. The welded zone of FSW joint is characterized with fine and equiaxed grains. With the increase of shoulder diameter, the cross section of weld zone perpendicular to the weld is enlarged and all the grains size of the welded zone, heat affected zone and thermo-mechanically affected zone increases. The dynamic recrystallization happens in thermo-mechanically affected zone of 5083 Al alloy at advancing side, which is different to the 6082 Al alloy at retreating side. The microhardness distribution presents a W shape and the minimum value locates at the heat affected zone. The result of microhardness agrees with the cross-section morphology of the welded zone.