In this study, underwater wet welding of 304L austenitic stainless steel to 16Mn low alloy steel was carried out using self-shielded flux-cored wires at a water depth of 0.3 m. The welds were produced using commercially obtained ER308 filler and specially developed nickel-based tubular wire. Microstructure and microhardness of wet welded joints have been particularly analyzed. The interface between austenitic weld metal and ferritic base metal was also discussed in detail. A robust weld of 304L/16Mn joint could be achieved by FCAW process using nickel-based tubular wire. Commercially obtained ER308 consumables failed to acquire sound welded joints due to large amount of slag remained in the groove. Ni-based weld metal was fully austenitic with well-developed columnar sub-grains while ER308 weld metal consisted of d-ferrite with different morphologies in the austenitic matrix. Type II boundary existed between austenitic weld metal and ferritic base metal. Compared to ER308 weld metal, Ni-based weld metal possessed the ability to be diluted by 16Mn base metal. Maximum hardness values in wet welding appeared in coarse-grained heat affected zone instead of transition zone for both consumables. Austenitic stainless steel welded joints exhibited high microhardness in the transition zone of 16Mn side, which was strongly diluted by ferritic base metal.