Conservation priorities are calculated on the basis of species richness, endemism, and threats. However, areas ranked highly for these factors may not represent regions of maximal evolutionary potential. The relationship between geography and evolutionary innovation was analyzed in a dominant complex of Caribbean reef corals, in which morphological and genetic data concur on species differences. Based on geometric morphometrics of Pleistocene corals and genetically characterized modern colonies, we found that morphological disparity varies from the center to the edge of the Caribbean, and we show that lineages are static at well-connected central locations but split or fuse in edge zones where gene flow is limited. Thus, conservation efforts in corals should focus not only on the centers of diversity but also on peripheral areas of species ranges and population connectivity.