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The genus <i>Telestes</i> primarily comprises freshwater fish distributed mostly in the Mediterranean area. Recent investigation of the evolutionary history of this genus revealed that it originated in southern Europe, where the most ancient <i>Telestes</i> species are still present. The isolation of rivers in the karstic region facilitated allopatric speciation, resulting in a high number of <i>Telestes</i> species and a great portion of endemic species in freshwater systems of Croatia and Bosnia and Herzegovina. Most of the endemic <i>Telestes</i> species have very small distribution areas, inhabiting a single river or a few water bodies in a single karstic field, making them extremely vulnerable to anthropogenic changes. In order to contribute to practical conservation of the endemic <i>Telestes</i> species through the design of conservational measures that are likely to be the most effective in ensuring the future viability and undisturbed evolutionary course of those species, we have investigated their population genetic structure and estimated their viabilities. Population viability analyses were carried out based on the current state of populations and their habitats, as well as recognized threats. Several scenarios also included potential threats. Our results show that invasive species pose the biggest threat to the future survival of the endemic <i>Telestes</i> species. Contrary to previous opinions that a reduced genetic diversity is characteristic for small populations, high intraspecific genetic diversity was revealed inside most of the investigated species, which might enable most of the populations to cope with future changes and mitigate negative effects.