Atlantic sturgeon (Acipenser oxyrinchus ssp. oxyrinchus) has been subjected to industrial-scale fishing activities, leading to multiple collapses of sturgeon stocks, driving populations such as those in the Chesapeake area close to extinction. Here, we investigate the genomic consequences of the population bottleneck in Atlantic sturgeon. This dataset comprises whole genome shotgun sequenced data from a single fin clip used for assembly of reference reads for target bait capture design.