Mesopelagic biogeographic boundaries in the open ocean are generally diffuse and coincident with meso-to-basin-scale physical oceanography. A notable exception occurs in certain topographic boundary regions, where spatially compressed midwater areas are constrained by 200-m and 700-m isobaths that may harbor ‘indicator’ mesopelagic species that are rare offshore and that exhibit behaviors influenced by the bottom. The presence of indicator species differentiates these ‘mesopelagic boundary communities’ (MBCs) from areas where oceanic deep-scattering layers impinge upon the continental slopes, but where the species composition is similar to that found offshore (although sometimes in high densities). MBCs have been well-documented over the upper slope of the Hawaiian Islands but have rarely been reported elsewhere. The possible reasons for the lack of MBC ubiquity are many, ranging from environmental to ecological to methodological. The last reason may be particularly important; for an MBC to be detected, a well-established offshore faunal inventory and/or behavioral catalog is necessary, against which uniqueness of a potential MBC fauna can be determined. Such inventories are lacking for much of the World Ocean. Here we will take a deep dive into the MBC phenomenon, comparing MBCs to other forms of topographic association (e.g., canyons, ridges), discussing requirements for maintenance of MBCs in a high dispersal environment, and presenting preliminary evidence of a possible MBC over a large deep-water coral complex in the Gulf of Mexico. We will finish by discussing the importance of MBCs for managed and/or protected marine species and for planning protected areas.