Understanding the evolution of marine biotas is a major goal in science, but little is know about the diversification of major groups of marine organisms on a global scale. To investigate the contribution of the deep-sea and shallow-water tropics to the formation of marine biotas, I used molecular phylogenetics and the fossil record to trace the evolutionary history of the second largest group of extant stony corals: the Stylasteridae. I sampled 100 of the 290 extant stylasterid species (in 20 of the 26 extant described genera) on a worldwide scale, and estimated their phylogenetic relationships using a 2638 base pair aligned DNA dataset. The results show that stylasterid corals originated and diversified in the deep-sea, and invaded the shallow-water tropics at least three times. The phylogenetic hypothesis provides the first compelling evidence that the deep-sea has contributed to the formation of shallow-water marine biotas. I also describe the first shallow-water stylasterid coral from the tropical eastern Pacific, and the first flexible stony coral. Finally, I revise the stylasterid genus Errinopora. Ten species of Errinopora are considered valid, four of which are described as new.