Coral reefs are the most diverse marine ecosystems on Earth and provide enormous economic value for hundreds of millions of people including fisheries, tourism, and coastal protection. However, these benefits are threatened by the rapid decline of coral reefs resulting from accelerating human impacts on local to global scales. Confronting this reef crisis with limited resources requires prioritisation of protection actions, and many researchers are now turning to reef ecosystems living outside of typical shallow, clear-water habitats as critical priorities for additional research. There is new evidence that these so-called marginal reefs living in turbid or deeper water can be more resilient to bleaching, changes in water quality, and other impacts. Increased bleaching resilience might result from sediments in the water that limit UV stress, or because the corals may be more readily able to take advantage of food sources in the plankton. Thus, marginal reefs potentially serve as refugia for resilient corals, and could be critical for the future recovery of declining clear-water reefs. However, most studies of marginal reefs have focused on contemporary (and in a few cases historical) assessments from sites on the Great Barrier Reef (GBR) and the Caribbean. New datasets from different regions are needed to capture the full range of modern human impacts (especially in areas of the most diverse coral development), and we also need data that spans the timescales (centuries to millennia) necessary to capture coral ecological adaptation and migration within marginal settings. In this context, recent discoveries of exceptionally preserved fossils from the Coral Triangle (CT) region of Southeast Asia provide a unique opportunity to integrate present-day ecological data with information from the geological record to document the evolutionary and ecological history of turbid water reefs in the modern-day global biodiversity hotspot. There is an urgent need for more information on the diversity, structure, and functioning of marginal reefs in the CT in order to help develop management strategies they continue to respond to human impacts. The long-term temporal scope of our study is thus significant. A growing body of research aims to describe the composition, distribution, and genetic structure of potential present-day reef refugia and we will add data from the fossil record into these analyses. There is a compelling case to do this because reef resilience is likely to be shaped by long-term processes with deep roots in evolutionary history. We will assess the dual role of marginal reefs in the CT as both cradles and refugia of diversity. Key research questions include: 1) has coral diversity of marginal ecosystems changed through time? 2) how have reef communities responded to environmental changes on regional or global scales? 3) how has reef functioning in marginal settings changed and what have been the consequences for reef-associated biota? 4) how easy has it been for reef-corals to move from marginal to clear-water reefs during the evolution of the biodiversity hotspot, and 5) what could be the consequences for the modern biota if clear water habitats become increasingly inhospitable? To address these questions we will produce new comprehensive datasets of species occurrences, abundances, morphological traits, ecological data, and environments that cover 30 million years of reef history of the CT. With this resource, we will provide rigorous answers to long-debated issues by applying new tools for molecular systematics, geochemistry, and evolutionary patterns to modern reefs and an extensive and well-sampled fossil record. Ultimately, we will be able to reveal the murky history of marginal reefs in the CT and better understand the potential future trajectories of change for coral reefs in the CT and in other regions that depend on coral reefs for their economic and ecological value.