Feral swine (Sus scrofa) are one of the most threatening mammalian pest species in North America owing to the damage they cause to natural habitats and agroecosystems, and the risk of disease transmission they pose to wildlife, livestock, and humans. The long-term (> 1 year) effects of lethal control efforts on feral swine populations at local scales are largely unknown. Using a panel of molecular markers, we assessed the effects of lethal control efforts on selected populations of feral swine in southern Texas. We collected tissue samples from two sites during removal campaigns, extracted and amplified DNA, and assessed population structure, genetic clustering, and immigration. We removed 145 individuals (9.7 swine per km²) at one site and 204 individuals (6.6 swine per km²) at another site. Fixation indices, Bayesian clustering, and assignment tests based on allele frequencies all produced similar results, indicating little or no differentiation among removals at either site.