Mesophotic coral ecosystems (MCEs) occur at depths beyond those typically associated with coral reefs. Significant logistical challenges associated with data collection in deep water have resulted in a limited understanding of the ecological relevance of these deeper coral ecosystems. We review the trends in this research, covering the geographic spread of MCE research, the focus of these studies, the methods used, how MCEs differ in terms of species diversity and begin to assess connectivity of coral populations. Clear locational biases were observed, with studies concentrated in a few discrete areas mainly around the Atlantic region. The focus of MCE studies has diversified in recent years and more detailed aspects of MCE ecology are now being investigated in particular areas of research. Advances in technology are also reflected in the current range of research, with a wider variety of methods now employed. However, large information gaps are present in entire regions and particularly in relation to the threats, impacts and subsequent management of MCEs. Analysis of species diversity shows that initial definitions based on depth alone may not be appropriate globally, while further taxonomic resolution may also be required to deduce the full biodiversity of major groups in certain regions. Genetic studies to date show species-specific results, although distinct deeper populations do appear to exist, which raises questions regarding the potential of MCEs to act as refugia.