Marine habitats are in decline worldwide, precipitating a strong interest in marine conservation. The use of biogeographic data to designate ecoregions has had significant impacts on terrestrial conservation efforts. However, classification of marine environments into ecoregions has only become available in the last several years, based on biogeographic data supplemented by geomorphology, ocean currents, and water temperatures. Here we use a comparative phylogeographic approach to test for concordant phylogeographic patterns in three closely related species of Tridacna giant clams across the Coral Triangle, the most biodiverse marine region in the world and one of the most threatened. Data from a 450 base pair fragment of mitochondrial cytochrome-c oxidase subunit one DNA from 1739 giant clams across Indonesia and the Philippines show strong concordance between phylogeographic patterns in three species of giant clams as well as evidence for potentially undescribed species within the genus. Phylogeographic patterns correspond broadly to marine ecoregions proposed by Spalding et al. (2007), indicating that processes contributing to biogeographic boundaries likely also limit genetic connectivity across this region. These data can assist with designing more effective networks of marine protected areas by ensuring that unique biogeographic and phylogeographic regions are represented in regional conservation planning.