The function and stability of mesophotic coral ecosystems (MCEs) have been extensively studied in recent years. These deep reefs are characterized by local physical processes, particularly the steep gradient in irradiance with increasing depth, and their impact on trophic resources. Mesophotic reefs exhibit distinct zonation patterns that segregate shallow reef biodiversity from ecologically unique deeper communities of endemic species. While mesophotic reefs are hypothesized as relatively stable refuges from anthropogenic stressors and a potential seed bank for degraded shallow reefs, these are site-specific features, if they occur at all. Mesophotic reefs are now known to be susceptible to many of the same stressors that are degrading shallow reefs, suggesting that they require their own specific conservation and management strategies.