Dissimilar friction stir welds of aluminum alloys AA5086 in annealed and AA6061 in T6 temper conditions were investigated in terms of residual stress, grain structure and precipitation distribution in different zones of the welded joints. Optical metallography and transmission electron microscopy were used to characterize microstructures of different zones of the welds. In addition, residual stress profile and local mechanical properties of different zones were evaluated employing X-ray diffraction method and digital image correlation technique. It was found that softening in the AA6061-T6 side occurs in regions with weld peak temperature higher than 300 A degrees C. The micro-hardness profile results and TEM investigations also showed that thermo-mechanical affected zone of AA6061 side with large plate-shaped beta precipitates is the softest region of the joints in AA6061 side. Furthermore, residual stress distribution within the samples is not directly dependent on the local mechanical properties of different zones of the joints.