Friction stir welding as a joining process in solid state welding various alloys widely used metal, particularly aluminum alloys. Although the low heat generated during the process does not melt the base metal, but the thermal cycle applied to the sample, which reduces the mechanical properties of the junction. Recently, this method of welding process is used in the cooling methods. In this study the microstructure and mechanical properties of 5050 aluminum alloy weld in two conditions: with friction stir welding in the air and on underwater friction stir welding was studied. The results of underwater friction stir welding were compared with samples of friction stir welding in the air. Results showed that the structure of the underwater welding was 36% more finely than welded structures in air and its tensile strength was improved about 6%. Also, the SZ zone in underwater friction stir welding has a higher hardness than friction stir welding in air.