Understanding the composition and functioning of subterranean habitats is particularly critical, as these ecosystems host a rich array of specialized, often endemic species that remain among the least explored and protected globally. We investigated the evolutionary history of endemic troglobiont beetles of the genus Trechus Clairville, 1806, from continental Portugal, that have been recently red listed as Critically Endangered and Endangered of extinction. We sequenced the mitochondrial cox1 gene of three species with restricted distributions: T. gamae Reboleira & Serrano, 2009, T. lunai Reboleira & Serrano, 2009, and T. tatai Reboleira & Ortuño, 2010. Our results show low genetic divergence among them and their hypothesized epigean common ancestor, T. fulvus Dejean, 1831. Despite this, consistent morphological differences, including reduced eyes and distinctive aedeagus shape, suggest divergent evolutionary trajectories and adaptations towards subterranean lifestyle. The unexpected lack of molecular differentiation points to a complex evolutionary history for this group of species. Future research should integrate additional molecular markers and expand taxonomic and geographic sampling, as this approach has the potential to enhance the identification of precise conservation units and, if necessary, improve existing strategies.