This research demonstrates the use of friction stir welding (FSW) to join dissimilar (Al-Mg) metal alloys. The main challenges in joining different, dissimilar metal alloys is the formation of brittle intermetallic compounds (IMCs) in the stir zone affecting mechanical properties of joint significantly. In this present study, FSW joining process is used to join aluminum alloy AA2139 and magnesium alloy WE43. The 9.5 mm thick plates of AA2139 and WE43 were friction stir butt welded. Different processing parameters were used to optimize processing parameters. Also, various weldings showed a crack at interface due to formation of IMCs caused by liquation during FSW. A good strength sound weld was obtained using processing parameter of 1200 rev/min rotational speed; 76.2 mm/min traverse speed; 1.5 degree tilt and 0.13 mm offsets towards aluminum. The crack faded away as the tool was offset towards advancing side aluminum. Mostly, the research was focused on developing high strength joint through microstructural control to reduce IMCs thickness in Al-Mg dissimilar weld joint with optimized processing parameter and appropriate tool offset.