The effect of friction stir welding (FSW) on the microstructure and localised corrosion behaviour of the dissimilar weld of AA2099 T83 and AA2060 T8E30 alloys is investigated. FSW results in a drastic change in the microstructure thus altering their corrosion behaviour. The heat-affected region exhibits similar attack morphology to their respective base metal but is the most protected region. The stir zone (SZ) is the most susceptible to attack. During immersion of the entire weld, attack initiation occurs from the AA2060 SZ due to galvanic activity within the region caused by the overlap of the grains in the weld zone.