Friction stir welding (FSW) would be effective as an underwater repairing process of the defective steel structures. In this study, underwater and conventional FSW trials were performed on 5.5 mm thick medium carbon steel at various welding parameters, and then the feasibility of underwater FSW to steels, and the microstructures and hardness profile of the welds were examined. Underwater FSW could produce defect-free welds, and exhibited higher torque and Z-axial load than conventional one. The stir zone was composed of ferrite and pearlite after conventional FSW, while underwater FSW produced a microstructure consisting of bainite with ferrite and pearlite in the stir zone, resulting in higher hardness than the conventional one. This difference could be explained by the cooling rate and the continuous cooling transformation diagram of the steel.