Friction stir welding is an advanced method of joining various metals and alloys in the aircraft and mechanical engineering industries. This type of welding is used to join materials that are difficult to weld or not weldable by conventional methods. The high-strength D16 aluminum alloy is difficult to weld by fusion, which is associated with the formation of a dendritic structure in the fusion zone leading to a decrease in the mechanical strength of the joint. In the work, the microstructure and microhardness of a welded seam of the D16 aluminum alloy produced by friction stir welding was studied. Using scanning electron microscopy and optical metallography, the authors identified the presence of three zones: the weld core, the thermomechanical impact zone, and the heat effected zone. In the central part of the welded joint (in the core), a laminated onion ring structure was discovered. A change in the chemical composition of the aluminum solid solution was identified in different areas of the weld zones, as well as the presence of a concentration gradient within each zone. In the upper part of the welded seam, the solid solution is silicon-enriched and depleted in copper. Due to the solid solution depletion in alloying elements, the aluminum content in the solid solution in the zone of the welded joint is higher compared to the initial state. The microhardness values in different areas of the welded joint correlate with changes in the chemical composition. In the welded joint zone, a significant decrease in microhardness was found compared to the initial state, and a change in microhardness associated with the chemical composition gradient within each zone was also observed.