Despite the presence of many cosmopolitan species in the ocean, patterns of connectivity across the deep-sea are still poorly understood. Widespread distributions have been documented for a number of prokaryotic and microscopic eukaryotic species (including deep-sea flagellates associated to hydrothermal vents), indicating their ability to disperse across the world’s oceans without being affected by geographic or distance barriers. Recent evidence has also pointed out that extensive gene flow seems to occur in cosmopolitan and bipolar deep-sea benthic foraminifera, which suggests that benthic deep-sea organisms may have the potential of dispersing over longer distances than previously thought. Regardless of the paucity of information on population genetics and dispersal of deep-sea marine invertebrates, a number of studies suggest that, although long oceanic dispersal is possible, distance barriers between suitable habitats can limit population connectivity. Deep-sea corals have particular environmental tolerances and habitat preferences that restrict their distributions. Whether the distribution of cosmopolitan benthic invertebrates correspond to present or past gene flow is a question that remains, for most species, unanswered.