Abstract The current research work aims to produce a defect free joint of Al6082 aluminum and AZ91 magnesium alloy sheets by friction stir welding (FSW) at various tool rotational and travel speeds with an objective to obtain the best combination of welding parameters to produce quality joint. The weld joint that was produced at the combination of 1400 rpm tool rotational speed and 30 mm min−1 feed exhibited defect free stir zone. Microstructural studies carried out in the weld joint demonstrated mechanical mixing of base materials from both the alloys in the stir zone. The mixing of Al6082 and AZ91 alloys was clearly appeared in the weld zone. It can be observed that the x-ray diffraction studies clearly demonstrated the development of intermetallics in the weld region. Higher hardness was observed for the joints that can be ascertained to the presence of more mixed regions in the stir zone that contains hard and brittle intermetallics. From the tensile test data, lower strength (175.71 ± 4.24 MPa) was observed for the weld joint compared with Al6082 (242. 6 ± 11.4 MPa) and AZ91 (205.27 ± 6.39 MPa) base materials. Furthermore, the ductility of the weld joint was measured as marginally higher than the AZ91 Mg alloy and lower than the Al6082 alloy. It can be concluded that the defect free weld joints of Al6082-AZ91 alloys can be successfully produced by FSW for structural applications targeted for dry environment.