Mesophotic coral ecosystems (MCEs), occurring at depths of 30 to over 150 m, represents the deep continuum of adjacent shallow coral reefs about which little is known. These reefs are most developed, and most frequently studied, in areas where light penetration is high and photosymbiotic reef-builders (corals) can persist as common members of the benthic community. The upper mesophotic zone typically extends to 60 m and comprises communities that are generally similar to those found in shallow reef systems. Below 60 m, the lower mesophotic zone is dominated by sponges and algae that are uncommon or absent from shallower areas, and a fish fauna that is largely specialized to these intermediate depths. It is likely that these ecosystems are much more widespread and important than was previously recognized. MCEs have the potential to function as refugia for shallow reefs because many disturbances in the upper 30 m may leave MCEs largely intact. Ontogenetic movement and spawning migrations by reef fishes provide an important ecological component to connectivity between shallow and mesophotic reefs and may represent the effective range of larval dispersal. However, there is currently limited information on genetic connectivity between deep and shallow coral reef populations, and this is a critical gap in understanding the role of MCEs in coral reef resilience. Here we review the connectivity and trophic relationships between the shallow and mesophotic coral reefs, the potential role of MCEs as refugia, and the effects of a new biological invader that exposes critical gaps in our understanding of the stability of these ecosystems.