Connectivity between coral reefs is critical to ensure their resilience and persistence against disturbances. It is driven by ocean currents, which often have very complex patterns within reef systems. Only biophysical models that simulate both the fine-scale details of ocean currents and the life-history traits of larvae transported by these currents can help to estimate connectivity in large reef systems. Here we use the unstructured-mesh coastal ocean model SLIM that locally achieves a spatial resolution of ~100 m, 10 times finer than existing models, over the entire Florida Reef Tract (FRT). It allows us to simulate larval dispersal between the ~1,000 reefs composing the FRT. By using different connectivity measures and clustering methods, we have identified two major connectivity pathways, one originating on the westernmost end of the outer shelf and the other originating on the inner shelf, North of the Lower Keys. We introduce new connectivity indicators, based on the PageRank algorithm, to show that protection efforts should be focused on the most upstream reefs of each pathway, while reefs best suited for restoration are more evenly spread between the Lower and Upper Keys. We identify one particular reef, North of Vaca Key, that is a major stepping stone in the connectivity network. Our results are the first reef-scale connectivity estimates for the entire FRT. Such fine-scale information can provide knowledge-based decision support to allocate conservation and restoration resources optimally.