Mesophotic coral reefs (MCRs) are an understudied continuum of shallow coral reef communities at depths of 30 to 150 m. These reefs are subject to gradients of light and nutrients that results in changes to the community structure and function with increased depth. The upper mesophotic reef is comprised of many of the same species that are found in shallow coral reef systems. However, the lower mesophotic reef, below about 60 m, has reduced photosynthetic biodiversity and often a replacement of corals and algae with sponges. The fish fauna is largely specialized to these intermediate depths, and to the available food resources. Thus, MCRs have the potential to function as refugia for shallow benthic reef species that are subject to disturbances in the upper 30 m of the water column. However, MCRs may be less stable than previously reported. Recent evidence from Caribbean reefs indicate that MCR community structure can change in as little as 3 years after decades of stability. Studies of fish spawning aggregations on MCRs have demonstrated the ecological importance of these sites to larval connectivity with shallow reefs, but recent evidence documents limited genetic diversity between MCR corals and shallow conspecifics. Despite site-specific differences in MCR community distribution and abundance, our data support a general model of structure and function that is equally applicable to MCRs in the Atlantic and Pacific.