Invasive species can impact native populations through competition, predation, and habitat alteration, but also genetically through hybridization. Potential outcomes of hybridization span the continuum from extinction to hybrid speciation and can be further complicated by anthropogenic habitat disturbance. Hybridization between the native green anole lizard (Anolis carolinensis) and a morphologically similar invader (A. porcatus) in south Florida provides an ideal opportunity to study interspecific admixture across a heterogeneous landscape of urban and forested habitats. We used reduced-representation sequencing to describe introgression in this hybrid system and to test for a relationship between urbanization and invasive ancestry. Our findings indicate that hybridization between green anole species was likely a limited, historic event, and that patterns of backcrossing have produced two distinct genetic clusters within the hybrid population. Genomic cline analyses revealed rapid introgression and disproportionate representation of invasive alleles at many loci, and no evidence for reproductive isolation between the two species. We also found a positive relationship between urbanization and invasive ancestry, although the mechanism driving this association remains unclear. Ultimately, our findings demonstrate the persistence of non-native genetic material even in the absence of ongoing immigration, indicating that selection favoring invasive alleles can override the demographic limitation of low propagule pressure. However, we also note that not all outcomes of admixture between native and invasive species should be considered intrinsically negative. Hybridization with ecologically robust invaders can lead to adaptive introgression, which may facilitate the long-term survival of native populations otherwise unable to adapt to anthropogenically mediated global change.