While substantial mesophotic coral ecosystem (MCE) habitat (>30-40 m) remains uninvestigated, recent investigations show that the extent of both MCE habitat and species diversity is greater than previously thought. The depth distributions and biogeographic ranges for many shallow-water organisms have also been historically underestimated. The upper mesophotic is home to many shallow-water marine organisms and represents a transition zone between shallow-water and lower mesophotic communities. The lower mesophotic represents a distinct community with some species exhibiting special physiological adaptations. Therefore, vertical connectivity is predominantly relevant between the upper mesophotic and shallow-water reefs. In some cases vertical connectivity is restricted due to genetic adaptation to these opposing reef habitats. Horizontal connectivity between MCEs remains largely unknown and represents an important avenue for future research.