The geographic structure of marine fish populations is an important element used in defining stock units, and genetic data have historically been used for this purpose. Here, genetic data were used to elicit population genomic patterns for Atlantic Croakers Micropogonias undulatus collected at five locations in the Gulf of Mexico (hereafter, “Gulf”) and a single location in the southern U.S. Atlantic. Mitochondrial DNA (mtDNA ) haplotypes were used as a baseline for historical lineage delineation and in a comparison with a previous Atlantic Croaker study that was centered on the Atlantic coast. A genomic data set consisting of 3,682 single‐nucleotide polymorphism (SNP )‐containing loci was used to assess contemporary gene flow throughout the sampled area. Both the mtDNA and SNP data sets showed significant between‐basin estimates of genetic divergence (ɸst = 0.049 and F ST = 0.002, respectively), while pairwise F ST implied a low magnitude of divergence (F ST ≤ 0.002) at all geographic scales. Comparison of patterns obtained from putatively “neutral” versus “outlier” SNP loci suggested contrasting genetic patterns at the extremes of the sampling distribution in the Gulf. Putatively neutral SNP s implied a single stock in the Gulf, whereas a handful of outliers suggested distinct populations in the eastern and western Gulf. The pattern observed at outlier loci could imply either the presence of natural selection impacting a small number of loci or otherwise could be explained as a remnant pattern reflective of historical geographic isolation. In either case, the weak population structure observed at a small number of SNP loci may be indicative of a more significant demographic structure; for this reason, caution is urged when treating Atlantic Croakers as a single stock in the Gulf.