The history of Scleractinian corals, richly documented by the fossil record, is one of complex dynamics linked to the dynamics of coral reefs themselves. In spite of all the waxing and waning of marine biodiversity throughout the post-Paleozoic, scleractinians have remained remarkably resilient as a lineage and have traversed two mass extinctions and repeated episodes of global change before becoming the chief builders of modern coral reefs. Understanding this history becomes all the more relevant in face of the current human driven coral reef biodiversity crisis. The advent of molecular phylogenetics has changed our perspective of those dynamics because it has uncovered pervasive morphological convergence in traditionally used taxonomic characters, revealing that the current classification is highly artificial. Taxonomy not only obscures important patterns, but also introduces artifacts into estimates of origination and extinction obtained directly from the fossil record. I present a brief review of the impact of molecular phylogenetics on the current understanding of coral evolution, with emphasis on the recently uncovered phyletic link between photosymbiotic, reef dwelling and azooxanthellate, deepwater coral biota. Then, I discuss the role of molecular-based techniques in a future research agenda of the evolutionary dynamics of the order. The greatest challenge for the future is the re-assessment of morphological characters from a cladistic perspective so that extinct and extant species are integrated in a unified phylogenetic framework, allowing rigorous testing of hypotheses on the fascinating biodiversity dynamics of the order.