Population connectivity refers to the exchange of individuals among populations: it affects gene flow, regulates population size and function, and mitigates recovery from natural or anthropogenic disturbances. Many populations in the deep sea are spatially fragmented, and will become more so with increasing resource exploitation. Understanding population connectivity is critical for spatial management. For most benthic species, connectivity is achieved by the planktonic larval stage, and larval dispersal is, in turn, regulated by complex interactions between biological and oceanographic processes. Coupled biophysical models, incorporating ocean circulation and biological traits, such as planktonic larval duration (PLD), have been used to estimate population connectivity and generate spatial management plans in coastal and shallow waters. In the deep sea, knowledge gaps in both the physical and biological components are delaying the effective use of this approach. Here, we review the current efforts in conservation in the deep sea and evaluate (1) the relevance of using larval dispersal in the design of marine protected areas and (2) the application of biophysical models in the study of population connectivity. Within biophysical models, PLD can be used to estimate dispersal distance. We propose that a PLD that guarantees a minimum dispersal distance for a wide range of species should be used in the planning of marine protected areas in the deep sea. Based on a review of data on species found at depths >200 m, a PLD of 35 and 69 days ensures a minimum distance for 50 and 75%, respectively, of eurybathic and deep-sea species. We note that more data are required to enhance accuracy and address the high variability in PLD between and within taxonomic groups, limiting generalizations that are often appealing to decision-makers. Given the imminent expansion of resource exploitation in the deep sea, data relevant to spatial management are needed urgently.