Deep-sea fishes remain poorly studied, due in large part to the difficulty of accessing the environment in which they reside. Genetic data for many deep-sea fishes is still absent or restricted to a small sample size from a limited geographic range. Here we collected DNA sequence data from the estimated 500 deep-sea fish species present in the pelagic environment of the Gulf of Mexico. Currently, 4700 individuals representing 481 species have been sampled using MOCNESS trawls sampling at as deep as 1500 meters. We used our molecular data to characterize the population genetic diversity and historical demography (i.e. population size changes) of these hundreds of fish species. This were done comparatively, so that species that differ in life history traits such as migration, feeding, generation time, and reproductive mode were contrasted with one another, and correlates between life history traits and population genetic parameters were tested. This allowed us to make inferences on how the life histories of hundreds of these understudied species contributes to the historical process that have generated the genetic diversity we observe today.