Within vertebrates, reptiles are good island colonisers, often leading to considerable levels of intraspecific diversity among populations inhabiting different islands/archipelagos. This study explores the mitochondrial phylogeographic structure of Tarentola boettgeri, a gecko species endemic to the Macaronesian archipelagos of Selvagens and the Canary Islands. Our research introduces a novel monophyletic group, comprising the populations from the islands of Selvagem Pequena and Ilhéu de Fora. Furthermore, we confirm the previously identified genetic clusters associated with Selvagem Grande, Gran Canaria and El Hierro. We estimate that the origin of T. boettgeri dates to the upper Miocene (ca. 6.4 Mya), and that the separation of T. boettgeri bischoffi on Selvagem Grande, Selvagem Pequena, and Ilhéu de Fora, occurred ca. 0.5 Mya. The absence of genetic differences between Selvagem Pequena and Ilhéu de Fora suggests recent gene flow or founder events, possibly facilitated by land connections during major glaciations. Conversely, the geographic barriers between Selvagem Grande and Selvagem Pequena likely persisted, preventing genetic admixing. The significant genetic distances observed among all populations underscore the necessity of an integrative taxonomic revision for T. boettgeri. In light of our findings, and with particular consideration of the small population sizes of T. boettgeri bischoffi on Selvagem Pequena and Ilhéu de Fora, we propose that the identified monophyletic groups should be managed as Evolutionarily Significant Units (ESUs). Accordingly, our study highlights the importance of recognizing ESUs in island-restricted reptile populations for targeted conservation efforts, especially given their unique intraspecific diversity and the vulnerability of their habitats.