Effective conservation of patchy marine habitats, such as those around islands, requires an understanding of ecological networks maintained through larval dispersal. In the Nansei Islands of Japan, previous studies suggested that the genetic connectivity of reef-building corals was independent of geographic distance along this near-linear island chain, likely due to the Kuroshio Current. However, this has not yet been confirmed using an integrated approach combining population genetics and physical oceanography. Here, we conducted biophysical modelling of larval dispersal and population genomic analysis across the Nansei Islands for a major reef-building coral, Acropora digitifera. Modelled larval dispersal networks showed that dispersal from the southern to northern ends of the archipelago occurred more than six times as frequently as dispersal to the central islands. Genetic differentiation between sites showed a stronger association with modelled dispersal (R = -0.44) than with geographic distance (R = 0.26). Kume Island served as a key stepping stone in the larval dispersal network, despite being outside the area’s national parks. This study provides fundamental insights into the dispersal pathway connecting distant locations along the Kuroshio Current—which we refer to as the ‘Kuroshio Corridor’—a concept that is crucial for connectivity-based conservation. The online version contains supplementary material available at 10.1038/s41598-026-40448-z.
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