The April 2010 Deepwater Horizon (DWH) oil spill released over 4 million barrels of oil into northern Gulf of Mexico ecosystems. Due to the magnitude of the spill and observed effects from previous spills, the ecological impacts were predicted to be catastrophic. While negative effects of petroleum hydrocarbon exposure to fish have been documented at the organismal scale, most studies of fish assemblages have noted few, if any, DWH impacts. Our understanding of DWH effects is therefore limited by a disconnect in results reported at different organizational levels. We used population genomic tools to test hypotheses about population-level DWH impacts to Gulf Killifish (Fundulus grandis) in coastal Mississippi. Fundulus grandis is one of the most abundant marsh species in the northern Gulf of Mexico, and along with the sister species F. heteroclitus, has served as a model for toxicology research. We collected genotyping by sequencing data from four populations of F. grandis (two oiled and two not) to test predictions about DWH-related gene flow, demographics, genetic diversity and evidence of selection. Mississippi populations of F. grandis showed clear genetic structure, but there were few indicators (e.g. reduced genetic diversity, lower Ne estimates) consistent with large-scale mortality or migration related to DWH oil. Only one estimate of effective population size was reduced in oil-exposed populations and of the twenty outlier loci only two were in regions with potential adaptive significance (i.e., immune functions). While the toxic effects of oil on F. grandis at the organismal level is well established, the minimal impacts we detected to populations along the Mississippi coast likely reflects the complexity of the northern Gulf of Mexico and DWH oil spill. However, we do recognize that the patchiness of oil exposure and low genome coverage of the data limit our ability to conclude there were no DWH effects on these populations.