The evolutionarily significant unit (ESU) is a conservation-oriented concept based on the principle of independently-evolving lineages but introgression may hamper definition of ESUs. Spatial proximity may lead to high levels of introgression and therefore affect identification of ESUs in the gecko Tarentola boettgeri within Gran Canaria, Canary Islands, where it is threatened by the introduced California king snake (Lampropeltis californiae). We sampled T. boettgeri from across Gran Canaria, El Hierro and the Selvagens archipelago. A 1.9 Gb T. boettgeri genome was assembled de novo from PacBio HiFi reads. Genotyping-by-sequencing (GBS) provided genomic sequences which were aligned to this reference genome to provide over 440 thousand SNPs in 134 geckos from 40 sample sites. Admixture analyses supported five genomic groups within Gran Canaria and two additional groups corresponding to the Selvagens and El Hierro. Phylogenomic analyses of both GBS sequences and SNPs revealed patterns consistent with ancient divergence followed by secondary contact and admixture within Gran Canaria. Unlike previous mtDNA estimates, our analyses suggest divergence within Gran Canaria began around the late Pliocene/early Pleistocene and colonization of the Selvagens and El Hierro occurred independently from north-western and western Gran Canarian lineages, respectively, during the Pleistocene. Bayesian multispecies coalescent analyses of Gran Canarian populations supported bidirectional introgression among all geographically adjacent lineages. Nonetheless, predominantly single ancestry populations were identified for all genomic groups within Gran Canaria despite their spatial proximity. We argue that these single ancestry metapopulations, and not introgressed populations, should be recognized as ESUs and be the focus of future efforts to conserve T. boettgeri biodiversity within Gran Canaria.