The everlasting desire of the manufacturing industries to produce more worthwhile products, by using innovative techniques, results in development of novel manufacturing processes. Friction stir welding, a kind of solid state processing is one of them. The aim of the present work is to examine the microstructural changes, microhardness and fatigue behavior of dissimilar aluminium alloys 5083 and 6063 welds by FSW. The joints are fabricated by using vertical milling machine setup under optimum welding parameters with rotational speed of 1560 rpm. Microstructural and mechanical properties such as fatigue and hardness of the welded joints were analyzed.