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 F_ST 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.

Nineteen microsatellite loci, obtained by the whole genome sequencing approach, were developed and validated for the ‘smooth cauliflower’ coral Stylophora pistillata, a widespread Indo Pacific branching coral species. A sample size of 40 colonies collected at five reef sites along the northern Gulf of Eilat, the Red Sea, were genotyped, revealing loci reproducibly and suitable outcomes for wide applications, including population genetic studies. The 19 new microsatellite loci in this sample were composed of 4–20 alleles/locus, of which 10 microsatellites are highly polymorphic (≥10 alleles/locus). The observed and expected heterozygosity ranged between 0.289 and 0.957 (mean 0.597) and 0.101 and 0.911 (mean 0.726), respectively, and the Fixation Index (F), which also indicates the inbreeding coefficient, ranges between −0.174 and 0.569 (mean 0.207). The polymorphic information content (PIC) ranges between 0.100 and 0.904 (mean 0.699). This new set of microsatellite loci will be employed for population genetics studies as for identifying the distribution of various genotypes within S. pistillata chimeras.

Accurate identification of scleractinian coral species is fundamental for proper biodiversity estimates, for aiding in efforts of reef monitoring, conservation, restoration, and for the management of coral reefs. Here, we provide the first DNA barcoding reference library for coral species in Eilat, Red Sea, based on the mitochondrial gene cytochrome c oxidase subunit I (COI), targeting the identification of stony coral species from shallow (0–12 m) reefs. A total of 191 specimens were collected, depicting 14 families, 39 genera, and 94 species (all are new full species records to the BOLD system). Three species (Sclerophyllia margariticola, Cyphastrea magna, and Psammocora profundacella) are first records for Eilat’s coral reef. The results presented here strengthen the claim that COI is not universally informative for delimitation of stony coral species, a notion reinforced by the constructed maximum likelihood phylogenetic tree. This library is the first step in a long journey towards elucidating coral biodiversity in the coral reef at Eilat and for improving future management and monitoring efforts.