The warming and acidification of the oceans, caused by rising levels of anthropogenic carbon dioxide, pose a serious threat to tropical coral reef ecosystems. We are currently studying the effects of these threats with our collaborators at the Palau International Coral Reef Center (www.picrc.org/, PICRC) and The Nature Conservancy (http://www.nature.org/ourinitiatives/regions/asiaandthepacific/micronesia/placesweprotect/the-republic-of-palau.xml, TNC), in Republic of Palau. We are developing new tools to quantify coral and coral community resistance and resilience to ocean acidification and thermal stress. Our approach provides a scientific basis for the identification of key refuges that have (a) greater potential to survive thermal and acidification stress and (b) provide larvae needed to reseed damaged or less resilient areas. Combining our approach with ecological considerations (connectivity, healthy populations of key functional groups), site-specific thermal history and global climate model projections of future changes, will assist in the development of indices of reef vulnerability that can be directly incorporated into the selection and design of marine protected area (MPA) networks.