Pressures and threats to shallow-water coral reefs have intensified over the last decades. The ‘Deep Reef Refuge’ Hypothesis (DRRH) postulates that Mesophotic Coral Ecosystems (MCEs) may be protected from these pressures and threats and could provide larvae to shallower reefs, therefore representing a genetic source for recolonising degraded shallow habitats. Focusing on the coral genus Pocillopora in Reunion Island (southwestern Indian Ocean), we aimed to (1) characterize the vertical distribution of each molecularly identified species, (2) determine their population structuring, to seek for evidence of vertical and horizontal connectivity in depth, and (3) test whether the DRRH may apply to these coral species in Reunion Island. We used 13 microsatellite loci to assess the genetic structure in Pocillopora populations sampled along a depth gradient (at 15, 30 and 45 m depth) on three sites around the island. Among the 288 colonies sampled, four species were identified, but only one (P. aff. verrucosa) was found in sufficient number at all depths for further analyses. Its populations showed no evidence of genetic structuring among sites and depths, highlighting strong vertical and horizontal connectivity at all depths. We argue that the shallow populations of P. aff. verrucosa could benefit from the larvae produced by MCEs in Reunion Island, therefore implying that MCEs can serve as a substantial reproductive refuge for this species. Nevertheless, complementary studies are needed to confirm these results, particularly focusing on other reef-building species with contrasting life-history traits and regions. This deposit contains the microsatellite genotypes of the Pocillopora samples analysed (288 individuals × 13 loci). Missing data are encoded as '?'.