The coral reefs of the South and Eastern Atlantic are impoverished in species diversity and abundance relative to the Caribbean because they occupy areas of suboptimal conditions for coral growth. Biodiversity and connectivity are important for the resilience and persistence of reefs, but corals inhabiting the periphery, or limits of the species range, lack the buffering qualities of ecological redundancy that accompanies biodiversity and may be isolated from sources of migrants that could replenish populations in the event of disturbance. Conversely, peripheral populations may be the site of divergence, local adaptation and speciation as a result of isolation. I explore the contributions of peripheral coral populations in Brazil and West Africa to preserving and generating biodiversity and their role in maintaining genetic connectivity across long distances in the Atlantic. Current estimates of coral biodiversity are confounded by pervasive morphological convergence, potentially underrating regional endemism. Molecular data presented here suggest that biodiversity has been underestimated for Mussismilia, a genus endemic to Brazil, and that the South Atlantic can be the site of species origination, such as for Favia gravida. Over ecological time scales, high connectivity provides a means for populations to persist in impacted locations by the influx of migrants from distant healthy reefs, while over longer time scales, isolation can be a creative mechanism that promotes diversification. I present the first molecular datasets that examine basin-scale dispersal in seven species of amphi-Atlantic corals. Isolation among regions is inferred for all but one species, indicating that coral populations must rely on regional recruitment to persist, but that local adaptation and future diversification may also take place. Within regions, however, differences in connectivity appear to be associated with reproductive mode. Among coral populations of Brazil, connectivity was greatest for broadcasting species and more restricted for brooding species, suggesting that aspects of reproduction may aid in dispersal at local scales. Peripheral coral reefs in the Atlantic are important sanctuaries for a host of endemic corals and other marine species and should be recognized for their distinctiveness, their role as sites of diversification, but also protected because of their isolation and vulnerability.