Understanding how genetic diversity is maintained across patchy marine environments remains a fundamental problem in marine biology. The Coral Triangle, located in the Indo-West Pacific, is the center of marine biodiversity and has been proposed as an important source of genetic diversity for remote Pacific reefs. Several studies highlight Micronesia, a scattering of hundreds of small islands situated within the North Equatorial Counter Current, as a potentially important migration corridor. To test this hypothesis, we characterized the population genetic structure of two ecologically important congeneric species of reef-building corals across greater Micronesia, from Palau to the Marshall Islands. Genetic divergences between islands followed an isolation-by-distance pattern, with Acropora hyacinthus exhibiting greater genetic divergences than A. digitifera, suggesting different migration capabilities or different effective population sizes for these closely related species. We inferred dispersal distance using a biophysical larval transport model, which helped explain an additional 15-21% of genetic variation compared to between-island geographic distance alone. For both species, genetic divergence accumulates and genetic diversity diminishes with distance from the Coral Triangle, supporting the hypothesis that Micronesian islands act as important stepping-stones connecting the central Pacific with the species rich Coral Triangle. However, for A. hyacinthus, the species with lower genetic connectivity, immigration from the sub-equatorial Pacific begins to play a larger role in shaping diversity than input from the Coral Triangle. This work highlights the enormous dispersal potential of broadcast-spawning corals and identifies the biological and physical drivers that influence coral genetic diversity on a regional scale.