An understanding of larval dispersal and connectivity in corals provides valuable insight into the processes of population maintenance and replenishment and is vital for effective management. Here, we used a genotyping by sequencing approach to explore patterns of genetic connectivity in two species of coral with different reproductive modes (brooding and broadcast spawning) at the Rowley Shoals in northwest Australia. Our data revealed strikingly different patterns of genetic structure in the two species. High levels of genetic subdivision in the brooding coral I. brueggemanni was consistent with extensive self-recruitment and restricted connectivity. In contrast, the broadcast spawning coral A. digitifera formed a single panmictic population with extensive gene flow. Our results highlight the wide variation in metapopulation connectivity that exists among corals and support the well-established link between reproductive mode and population genetic structure in the marine environment.