Refugia can facilitate the persistence of biodiversity under changing environmental conditions, such as anthropogenic climate change, and therefore constitute the best chance of survival for many coral species in the wild. Despite an increasing amount of literature, the concept of coral reef refugia remains poorly defined; so that climate change refugia have been confused with other phenomena, including temporal refuges, pristine habitats and physiological processes such as adaptation and acclimatization. We propose six criteria that determine the capacity of refugia to facilitate species persistence, including long-term buffering, protection from multiple climatic stressors, accessibility, microclimatic heterogeneity, size, and low exposure to non-climate disturbances. Any effective, high-capacity coral reef refugium should be characterized by long-term buffering of environmental conditions (for several decades) and multi-stressor buffering (provision of suitable environmental conditions with respect to climatic change, particularly ocean warming and acidification). Although not always essential, the remaining criteria are important for quantifying the capacity of potential refugia.