Coral reefs are considered among the most important marine ecosystems and host a wide range of species, but in most habitats, including the Persian Gulf, they are under serious threat due to several factors such as human activities and climate change. The formation of coral reefs is due to the symbiosis of a type of symbiotic microalgae that plays an important role in providing organic matter and calcium carbonate sediments for corals. This study investigates and molecularly identifies symbiotic microalgae associated with 17 species of reef-building corals collected from Shidvar Island: Porites lobata, Dipsatrea pallida, Porites compressa, Dipsatrea matthaii, Acropora downingi, Platygyra daedalea, Plesiastrea versipora, Cyphastrea serailia, Cyphastrea microphthalma, Leptastrea transversa, Platygyra sinensis, Porites sp., Pavona decussata, Psammocora stellata, Favites pentagona, Anomastrea irregularis, and Acropora arabensis. DNA was extracted using the Chloroform-CTAB method and the target gene ITS2 was amplified with a zooxanthellae-specific primer. Then, the PCR product was sequenced and a Bayesian phylogenetic tree and maximum likelihood were constructed using MrBayes and Mega5 software. Phylogenetic results showed the dominance of the heat-resistant clade D, especially subclade D1a, followed by clade C1, and the presence of clade A in Leptastrea transversa. The dominance of clade D, which seems natural due to its high resistance to thermal stresses, highlights the adaptation and resistance of the Persian Gulf corals to high temperatures, salinity fluctuations, and other stressors.