Coral reefs are among the most biodiverse and productive ecosystems on the planet. However, our understanding of these ecosystems and their inhabitants has primarily been gleaned from shallow-water studies (<40 m), while light-dependent corals and the ecosystems they support extend much deeper (e.g., 150 m in some locations). In recent decades, coral reef ecosystems have substantially declined globally due to direct and indirect anthropogenic activities that differentially impact shallow-water habitats. This decline has led to the suggestion that surface-oriented stressors and disturbances may be mediated by depth. The role of deeper coral reef ecosystems, called mesophotic coral ecosystems (MCEs), as refugia for shallow-water species has fueled new investigations into this realm facilitated in part by advances in diving technology and remote observation platforms. The increasing access to these poorly studied ecosystems is revealing new insights into the biodiversity of MCEs as well as that of shallow coral reefs. The upper mesophotic community is largely an extension of the shallow-water coral reef community, much of the flora and fauna are shared across these depths. However, there is a transition with increasing depth to a lower mesophotic community dominated by flora and fauna that are largely endemic to this zone. Investigations are also expanding depth and geographic ranges for many species, and new species are being discovered regularly in MCEs. However, caution must be taken when generalizing due to the geographically and numerically limited nature of these studies.