The Gulf of Mexico experiences frequent perturbations, both natural and anthropogenic. To better understand the impacts of these events, we must inventory natural variability within the ecosystem, communities, species, and populations, and contextualize these findings in relation to physical features. This data is part of a comparative population genomics study targeting three species of mesopelagic shrimp common to the Gulf</p><p>of Mexico midwater (Acanthephyra purpurea, Systellaspis debilis, and Robustosergia robusta). We analyzed genetic diversity and population connectivity as proxies for species health and resilience, respectively, with the goals of establishing biological baselines and characterizing these values in terms of the prevailing oceanographic feature of the midwater: the Gulf Loop Current.