Habitat connectivity is central to several key evolutionary and ecological processes, having implications for the spatial structuring of marine populations. For benthic species that have no or little mobility as adults, connectivity is evaluated by analyzing the dispersal of propagules across the seascape. We investigate fine-scale connectivity of coralligenous habitats in Marseille Bay (located in the north-western Mediterranean) sea using high-resolution cartography and a particle-tracking model ran over a range of parameters derived from the biological traits of potential target species. We present annual and seasonal means of various connectivity diagnostics measuring the retention and exchange of propagules among coralligenous patches. A synthetic view is obtained by clustering individual patches into “coralligenous provinces” (ensemble of patches tightly connected by ocean currents). When discussing our results against historical observations, we highlight some genetic breaks, sharp community changes and ecological clusters that fit well our simulated connectivity patterns. Consistent findings include reduced biodiversity along Côte Bleue, high biodiversity at Planier Island and the presence of various dispersal barriers, which evolve with dispersal durations and provide the backbone of habitat connectivity. Our results help to apprehend and test hypothesis on marine population structures, providing useful information for ecologists and conservationists.