Seamount systems that are geographically, hydrographically, topographically, and/or genetically “isolated” are likely to have developed highly endemic taxa and ecosystems. Although current estimates of endemism are challenged by inconsistencies in sampling approaches, the physical, biological, and geological processes intrinsic to seamount systems can undeniably serve to connect or isolate populations, stimulate genetic divergence, drive the formation of new species, and structure diversity and endemism. In fact, the large variety of interconnected mechanisms that promote or impede the genetic connectivity of seamount communities via dispersal (and the long-term maintenance of species or the subsequent divergence of populations leading to speciation) are key unknowns to understanding the fundamental evolutionary processes that structure both the diversity and biogeography of deep-sea fauna. Fortunately, the net results of these ecological interactions at seamounts are represented in the patterns of genetic connectivity of the constituent species. The conclusions of the relatively few genetic connectivity studies across seamount fish, coral, and invertebrates are largely inconsistent, reflecting the ecological and evolutionary complexities of seamount systems. Yet, identifying the “connectivity” of seamount populations and their diverse ecosystems, which are increasingly vulnerable to threats from destructive fisheries and mining practices, is vital for developing and evaluating conservation and management strategies for seamount resources. Integrated, multidisciplinary studies of the physical, chemical, geological, an ecological dynamics of seamounts will continue to reveal the value of seamounts as natural laboratories in which to gain insights into the factors that elucidate the role these systems play in the dispersal, evolution, and biodiversity of deep-sea fauna. These studies will also direct the management of seamount biological diversity, which is increasingly susceptible to anthropogenic disturbance.