Mesophotic coral ecosystems (MCEs) are characterized by the presence of light-dependent corals and associated communities that are typically found at depths ranging from 30 to 40 m and extending to over 150 m in tropical and subtropical regions. The dominant communities providing structural habitat in the mesophotic zone can be comprised of coral, sponge, and algal species. Because working in this depth range is constrained by traditional SCUBA limits, less is known about corals and associated organisms there compared to shallower coral communities. Following the first-ever gathering of international scientists to review and discuss existing knowledge of MCEs, this issue focuses on the ecological characterization, geomorphology, and concept of MCEs as refugia for shallow-water populations. The review and research papers comprising this special issue reflect the current scientific understanding of these ecosystems and the underlying mechanisms that regulate them, as well as potential resource management implications. It is important to understand the value and role of mesophotic coral ecosystems in tropical and subtropical regions as these areas face increasing environmental change and human impacts.