We addressed the evolutionary history of Tridacna giant clams by combining molecular phylogenies with the geographic distribution of lineages across the Indo-West Pacific, with a focus on the Western Indian Ocean (WIO). A giant clam initially identified as T. maxima was genetically distinct and identified as T. elongatissima, a long-forgotten species from Mozambique. Two nominal species endemic to the Mascarene basin, T. lorenzi and T. rosewateri were found to be a single and same, distinct species. Tridacna elongatissima turned out to be the sister species of T. squamosina, another recently resurrected species endemic to the Red Sea. The T. elongatissima-T. squamosina pair was itself sister to T. rosewateri, highlighting this part of the world as a hotspot of endemism for giant clams. With two unrelated lineages in the WIO, one of which was sister to a third lineage endemic to the Red Sea, lineage diversification patterns within the widespread T. maxima mirrored those of T. elongatissima, T. rosewateri and T. squamosina. The same geographic barriers and speciation processes may thus have acted repeatedly at different periods in the Pleistocene.