This dissertation characterizes the genetic diversity and thermal tolerance of the coral holobiont Stylophora pistillata and Pocillopora verrucosa (family Pocilloporidae) across the Saudi Arabian Red Sea coast (~1500 km). The population genetic structure and holobiont diversity was assessed using genome-wide single nucleotide polymorphisms (SNPs) identified with reference genome-based RAD-Seq, while the associated microbial communities of the algal symbiont (Symbiodiniaceae) and bacteria were inferred from metabarcoding analyses of the ITS2 and 16S rRNA gene. Thermal tolerance of Stylophora pistillata colonies was assessed using standardized short-term heat stress assays on the novel Coral Bleaching Automated Stress System (CBASS). Chapter 1 details the assembly and annotation of the P. verrucosa genome (~380 Mbp; 27,439 gene models), which was highly complete and compared well to the already available S. pistillata genome. Chapter 2 presents population genetic analyses of both coral species, which revealed pronounced differences in their population genetic structure. While P. verrucosa seemed to be highly connected across the Red Sea basin with the exception of the far south, S. pistillata depicted a complex population genetic structure. Microbial communities of Symbiodiniaceae and bacteria were overall less diverse in P. verrucosa than in S. pistillata, and followed an association pattern that was partly determined by the environment and partly by host genotype. Chapter 3 identifies thermally tolerant S. pistillata genotypes by comparing the heat stress response of colonies collected at two sites within the same reef. Ex-situ heat-stress assays confirmed that colonies from the more temperature stable site (fore reef) were less thermally tolerant than their conspecifics from the back reef, where the diel temperature is more variable. This chapter also highlights the utility of acute heat-stress assays as a tool to identify thermotolerant colonies. Taken together, the work of this dissertation provides a foundation for coral conservation in the Red Sea. It highlights that the genetic structure differs between coral species, suggesting that effective conservation through marine protected areas need to incorporate data from multiple species. Coral population genetic data should further be complemented by thermal tolerance assays across the Red Sea to associate genetic diversity with patterns of heat stress tolerance.