Over the last seven years, the Florida Reef Tract (FRT) has been experiencing an outbreak of the Stony Coral Tissue Loss Disease (SCTLD). First reported off the coast of Miami-Dade County in 2014, the SCTLD has since spread throughout the entire FRT and continues to propagate throughout the Caribbean. Although the causative agent for this disease is currently unknown, the hydrodynamics is highly explanatory of the SCTLD patterns of infection. The same hydrodynamics is also the driving mechanism of coral larvae dispersal and coral connectivity, which enhance the overall system resilience. Connectivity therefore appears to be a double-edged sword as it can both enhance and degrade coral populations. In the present study, we try to disentangle the respective effects of disease and larval connectivity in order to identify reefs best suited to restoration projects. We do that by computing larval and disease connectivity for three coral species in the entire FRT with a high-resolution biophysical model. Connectivity information is computed over 3 consecutive years and then analyzed using graph theory tools. This approach allows the development of reef-specific metrics to identify reefs with a high restoration potential for different degrees of disease susceptibility. These are the reefs that are both good larval suppliers and weak potential sources of disease agents. Using this indicator, we construct species-specific maps indicating reefs with best restoration potential for different disease susceptibilities, hence allowing the identification of favorable outplant sites with low probability of infection. These maps can support ongoing restoration projects and indicate for instance that some reefs selected for the “Restoring Seven Iconic Reefs” mission (Horseshoe Reef and Looe Key) are poorly protected against the SCTLD. Our model is further able to reproduce the observed slow-down of the disease propagation in the Florida Keys in 2020, and suggests that the Dry Tortugas were infected only in November or December 2020. By combining both larval and disease connectivity, this study has the potential to support restoration efforts in Florida by designing effective management strategies against the worst coral epidemic on record in the Caribbean.