In this study, plates of AL-6XN and 316L stainless steels were gas metal arc welded with an ER-NiCrMo3 filler wire and the effect of two different heat inputs and different accumulated fatigue damage is evaluated in terms of microstructure and mechanical behavior. Microstructural characterization of the as-welded samples revealed differences in dendrite size and interdendritic spacing in the weld metal with respect to the side of the dissimilar weld and to the heat input that results in weld metal regions with strong texture. Mo–Nb rich particles were found in the weld metal for both welding conditions and high heat input yielded very wide unmixed zones. Failure of the as-welded samples, under tensile stress, consistently occurred in the 316L base metal irrespective of the heat input. However, it was found that for a high heat input (1.6kJ/mm) accumulated fatigue damage changed the mechanical response of the welded dissimilar joints so that fracture took place in the weld metal. Ultrasonic attenuation measurements were used to characterize the welded joint and results showed regions of high attenuation that are related to dendritic structures.