Aim: The aim of the study was to assess the diversity of algal symbionts of the family Symbiodiniaceae associated with the coral genus Porites in the Red Sea, and to test for host-specificity and environmental variables driving biogeographical patterns of algal symbiont distribution. Location: Saudi Arabian Red Sea. Taxon: Endosymbiotic dinoflagellates of the family Symbiodiniaceae in association with the reef-building coral genus Porites. Methods: Eighty Porites coral specimens were collected along the Saudi Arabian Red Sea coast. Species boundaries were assessed morphologically and genetically (putative Control Region – mtCR; ITS region – ITS). Community composition of symbiotic dinoflagellates of the family Symbiodiniaceae was also assessed. Using the ITS2 marker with the SymPortal framework, Symbiodiniaceae data at the genus, majority ITS2 sequence and ITS2 type profile were used to assess symbiont diversity and distribution patterns. These were analysed in relation to coral host diversity, geographic location and environmental variables. Results: Among the 80 Porites samples, 10 morphologies were identified. These corals were clustered into five lineages (clades I–V) by each of the markers independently. Clades I, II and III each comprised of a single Porites morphology, while clades IV and V contained up to five distinct morphologies. The diversity of Symbiodiniaceae associated with Porites was high and latitudinal differentiation was observed. In particular, a shift from a Cladocopium-dominated to a Durusdinium-dominated community was found along the north–south gradient. Symbiont diversity showed the patterns of geographic-specific association at Symbiodiniaceae genus, majority ITS2 sequence and ITS2 type profile level. Specific associations with host genotypes (but not morphological species) were also recovered when considering Symbiodiniaceae majority ITS2 sequence and ITS2 type profiles. Main conclusions: This study provides the first large-scale molecular characterization of Symbiodiniaceae communities associated with Porites corals from the Saudi Arabian Red Sea. The use of intragenomic diversity data enabled the resolution of host-symbiont specificity and biogeographical patterns of distribution, previously unachievable with the ITS2 marker alone. Finally, correlation among symbiont diversity and Red Sea environmental gradients was documented.