Farm site selection plays a critical role in determining the productivity, environmental impact, and interactions of aquaculture activities with ecosystem services. Satellite Remote Sensing (SRS) provide spatially extensive datasets at high temporal and spatial resolution, which can be useful for aquaculture site selection. In this paper we mapped a finfish aquaculture Suitability Index (SI) applying the Spatial Multi-criteria Evaluation (SMCE) methodology. The robustness of the outcome of the SMCE was investigated using Uncertainty Analysis (UA), and in parallel we evaluate a set of alternative scenarios, aimed at minimizing the subjectivity associated with the decision process. The index is based on the outputs of eco-physiological models, which were forced using time series of sea surface temperature data, and on data concerning Significant Wave Height (SWH), distance to harbor, current sea uses, and cumulative impacts. The methodology was applied to map the suitability for farming of European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata) within the Italian Economic Exclusive Zone (EEZ), under three scenarios: Blue Growth, Economic and Environment. Tyrrhenian and Ionian coastal areas were found to be more suitable, compared to the Northern Adriatic and southern Sicilian ones. In the latter, and in the western Sardinia, the index is also affected by higher uncertainty. The application presented suggests that SRS data could play a significant role in designing the Allocated Zones for Aquaculture, assisting policy makers and regulators in including aquaculture within maritime spatial planning.