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The successful management of coral reefs necessitates understanding the genetic characteristics of reefs' populations since levels of genetic diversity play a critical role in their resilience, enabling them to withstand environmental changes with greater efficacy. To assess the genetic diversity and connectivity of the widespread Indo-Pacific coral, Stylophora pistillata, eight microsatellite loci were employed on 380 tissue samples collected from eight sites along the northern Gulf of Eilat, Red Sea. We documented deviations from the Hardy–Weinberg equilibrium and observed low heterozygosity and high values of expected heterozygosity (0.59 and 0.82, respectively). The relatively high FST values and STRUCTURE analysis results showed population fragmentation along the short coastline (<12 km). These results signify isolation by distance, low gene flow between most populations, and possible non-random mating. These results are connected to this species' sexual reproduction traits, a brooding coral species with planulae that settle shortly upon release with limited connectivity that are most probably further exacerbated by anthropogenic impacts imposed on Eilat's reefs. This study provides insights into the connectivity and population genetics of S. pistillata residing in an urbanized northern Red Sea reef and reinforces the need for better management of the current MPA, employing future active coral reef restoration in the area. [ABSTRACT FROM AUTHOR]