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Invasive species can impact native populations through competition, predation, habitat alteration, and disease transmission, 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. We used reduced‐representation sequencing to describe introgression in this hybrid system and to test for a relationship between urbanization and non‐native ancestry. Our findings indicate that hybridization between green anole lineages was probably a limited, historic event, producing a hybrid population characterized by a diverse continuum of ancestry proportions. Genomic cline analyses revealed rapid introgression and disproportionate representation of non‐native alleles at many loci and no evidence for reproductive isolation between parental species. Three loci were associated with urban habitat characteristics; urbanization and non‐native ancestry were positively correlated, although this relationship did not remain significant when accounting for spatial nonindependence. Ultimately, our study demonstrates the persistence of non‐native genetic material even in the absence of ongoing immigration, indicating that selection favouring non‐native alleles can override the demographic limitation of low propagule pressure. We also note that not all outcomes of admixture between native and non‐native 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.