The attenuation of light with increasing depth, along with reduced exposure to wave stress, plays an important role in vertically structuring coral reef communities. Benthic photosynthetic organisms exhibit different depth distributions and abundance patterns which cause changes in community composition of associated reef fauna. This vertical zonation in coral reef community structure suggests special adaptations in response to the changing environmental regime with depth including changes in light intensity, light spectrum, and angular distribution. At the lower depth limits of mesophotic coral ecosystems (MCEs), both light and temperature can become limiting factors with the latter playing an important role at higher latitudes. The available evidence indicates that different species can exhibit distinct and sometimes opposing photophysiological adaptations with increasing depth. Some zooxanthellate corals appear to maximize ambient light utilization at the expense of efficiency, while others appear to maximize efficiency. Coral holobiont adaptations to mesophotic depths include changes in colony morphology, algal symbionts, pigment physiology, skeletal properties, and metabolic strategy. Given the scarcity of physiological studies at depths >60 m, the current understanding of how obligate zooxanthellate corals and other light-dependent organisms can inhabit such a broad depth distribution is far from complete. This chapter summarizes the ecologically relevant aspects of light and temperature regimes of MCEs, as well as the depth-related photophysiological and adaptive strategies of coral holobionts.