We have become increasingly aware that introgression, interspecific gene flow via hybridization, is a widespread phenomenon across the tree of life. Introgression occurs most frequently between closely related sister-species and eventually ceases or results in the fusion of lineages. Yet, in contrast with this view, instances of hybridization are occasionally recorded among distantly related taxa and can even occur between non-sister species. It remains unclear whether introgression in such situations is evolutionary meaningful and results in the actual exchange of functional variants or whether the degree of nuclear introgression is negligible. To address this question, further empirical examples are required that span the evolutionary timescales along which introgression continues to proceed. Here we focus on a group of Australian lizards and explore patterns of interspecific introgression in both a temporal and ecological framework. We focus on three species pairs within the genus Cryptoblepharus, where cytonuclear discord varies from complete fixation of an alternative mitochondrial haplotype to no cytonuclear discord at all. We employ a genomic approach (exon-capture) to generate a large number of orthologous loci and utilize both sequence and SNP based approaches to infer the genealogical history of individual loci. Overall, this study examines whether (ancient) introgression can result in pervasive patterns of nuclear haplotype sharing, regardless of phylogenetic distance or ecological differentiation, and evaluates its functional relevance.