Giant clams, the largest marine bivalves, are important coral reef engineering species. However, the giant clam population in the Red Sea has plummeted since 1980’s. Knowledge on their genetic distribution can facilitate the development of transboundary management plans to conserve these species. The analysis based on 501-bp fragment of the cytochrome oxidase I gene from 194 individuals (126 new sequences from current study plus 68 sequences from GenBank), collected from 14 locations in the Red Sea and Gulf of Aden, suggests the presence of one large, panmictic population across a wide range of temperature and salinity gradients in this region (global PhiST value of 0.02, p > 0.05). The genetic homogeneity could be attributed to the mode and time of reproduction as well as the ability of T. maxima to achieve high fitness in the highly variable environmental conditions of the Red Sea. Despite this, the population in Djibouti was genetically differentiated from the other 11 populations in the Red Sea, suggesting a connectivity break between the Red Sea and the Gulf of Aden. These results could be explained by the oceanographic features facilitating wide larval transport inside the Red Sea, and creating a dispersal barrier to the Gulf of Aden.
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