The Red Sea is a challenging environment for many marine organisms. It has one of the highest salinity concentrations (up to 40.2 ppt) and is the northernmost tropical sea worldwide. Due to almost complete isolation from the world’s oceanic system it is additionally a very unique region in terms of biodiversity and a potential species incubator. The 2,000 km long (N/S) but narrow (W/E) basin, pushes strong latitudinal environmental changes especially regarding salinity (40.2–37.5 ppt) and temperature (28–33.8°C), which are the main stressors for most marine invertebrates and drivers of adaptive strategies. Nevertheless, its waters harbor a species rich and diverse environment, which is still widely unexplored. To assess the impact of the temperature and salinity gradient on the connectivity of reef organisms, the abundant reef-building coral Pocillopora sp. was sampled from North, Central and South offshore reefs. Ten out of fourteen microsatellite markers available for Pocillopora spp. were employed on individuals to detect the presence or absence of an underlying population genetic structure. To assure the exclusion of putative cryptic species, specimen used in this study were chosen from a single mitochondrial lineage. Samples were taken off the coast of Saudi Arabia and the sampled area covered over 850 km from North to South. Despite the long distances between collection sites, no significant genetic population structure was found, rejecting possible subdivision of the species driven by environmental factors and suggesting rather panmixia and sufficient gene flow (FST = 0.0005, p = 0.340; Variance among sites = 0.0%, based on 9 loci). This result is striking considering additional seasonal temperature fluxes from over 6°C and suggests high tolerance levels of Pocillopora sp. to diverse environmental conditions. Moreover, maintaining genetic diversity and frequent larval dispersal over wide distances and among contrasting habitats further supports the adaptive potential and reproductive success of Pocillopora species worldwide.