Coral reefs are, per unit area, the most productive and diverse ecosystems on the planet. Their complexity and, in some places, fragility provide many complications to scientists conducting high quality research in these environments. Scientific diving has been, for the past six decades, a highly cost-effective and productive tool in coral reef research. Using high impact outputs and based mainly on the research supported through the diving programmes of the Smithsonian Institution, this review outlines some major scientific advances that have been made in coral reef research because of the support or use of SCUBA. The main areas of interest reported here are: algal sexual reproduction on coral reefs, coral spawning, conservation biology, coral diseases and declines, biodiversity, keystone species, biogeography of reef fishes, and DNA barcoding. The review concludes that significant advances in many areas of coral reef research were only achievable through diving-based approaches.