Wild-caught Syngnathus scovelli from a single population in the Gulf of Mexico near Corpus Christi, TX. A total of 228 individuals (females, pregnant males, and non-pregnant males) were collected and sequenced, along with 130 offspring from pregnant males' pouches. Other data are archived on Dryad (http://dx.doi.org/10.5061/dryad.5c1tj) and all the code is archived at https://zenodo.org/badge/latestdoi/51270799. These data accompany the paper "Genome-wide selection components analysis in a fish with male pregnancy" by Flanagan & Jones in Evolution.