Ecological impacts of invasive plant species are well documented, but the genetic response of native species to invasive dominance has been often overlooked. Invasive plants can drastically alter site conditions where they reach dominance, potentially exerting novel selective pressures on persistent native plant populations. Do native plant populations in old exotic invasions show evidence of selection when compared to conspecific populations in adjacent, noninvaded areas? We employ amplified fragment length polymorphism (AFLP) analysis to screen a large number of loci from two native grass species (Hesperostipa comata (Trin. & Rupr.) Barkworth and Sporobolus airoides Torr.) that occur in old infestations of the invasive forb Acroptilon repens. We then compare observed locus by locus FST values with distributions of FST estimated from simulation models under expectation of neutrality. We also compare the proportion of loci possibly linked to selection and those not linked to selection which exhibit parallel trends in divergence between two community types (invaded, noninvaded). Few loci (H. comata, 2.6%; S. airoides, 8.7%) in the two native grasses may be linked to genes under the influence of selection. Also, loci linked to selection showed a greater portion of parallel trends in divergence than neutral loci. Genetic similarities between community types were less than genetic similarity within community types suggesting differentiation in response to community alteration. These results indicate that a small portion of scored AFLP loci may be linked to genes undergoing selection tied to community dominance by an invasive species. We propose that native plants in communities dominated by exotic invasives may be undergoing natural selection.