Despite the ecological importance of deep-sea cephalopods, little is known about their genetic diversity or population dynamics. The cephalopod species Cranchia scabra, Pyroteuthis margaritifera, and Vampyroteuthis infernalis are commonly collected in midwater samples from both the Gulf of Mexico and northwestern Atlantic Ocean. Despite their common appearance in trawls and important roles in marine food webs, no genetic studies of population connectivity exist for these species. Here, ddRADseq was used to examine the population dynamics in these deep-sea species.