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Reef-building coral harbor communities of photosynthetic taxa of the genus Symbiodinium (zooxanthellae). The genus Symbiodinium is currently classified into nine genetic clades (A–I). Various corals harbor different Symbiodinium clades; some show specificity to a single strain. Coral and their zooxanthellae are sensitive to environmental stresses. In the Persian Gulf, coral reefs are subject to harsh environmental conditions including extreme temperatures and high salinity. This is the first study to use clade specific primers to clarify the diversity of Symbiodinium in each coral species of Larak Island. For this purpose six coral species were collected at two different locations in Larak Island. After DNA extraction, PCR amplification was performed using clade specific primers. The results showed that multiple Symbiodinium clades are hosted by most coral species. In addition, among thirteen obtained Symbiodinium sequences, the frequency of either tree clades, A, C and D was almost the same. Corals species may contain different clades of Symbiodinium depending on the region and on the tolerance characteristics of each clade. Thus, knowledge of zooxanthellae diversity associated with scleractinian can contribute to a better understanding of the sensitivity of corals to environmental conditions.