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Background: Together with other elevated areas, the Mountains of Central Asia are significantly threatened by ongoing climate change. The presence of refuges during the glaciations makes the region extremely rich in species, especially endemic ones. However, the limited potential for colonisation of other habitats makes rocky-related species with 'island-like' distribution, particularly vulnerable to climate change. To understand the processes underlying species response to climate warming, we assessed differences in ecological niches and phylogenetic relationship of two geographically disjunctive alpine species belonging to the genus Sergia. The taxa are considered Tertiary relicts, endemic to the Tian Shan and Pamir-Alai Mountains. To illustrate range dynamics and differences in occupied niches of Sergia species, we used Ecological Niche Modelling of current and future distribution. Whereas, to reconstruct the phylogenetic relationship within and between Sergia and other related Campanulaceae species from the region we used molecular data (ITS, cpDNA, DArTseq-derived SNPs)., Results: The results reveal that the genus Sergia is a polyphyletic group, and its representatives differ geographically, ecologically and genetically. Both S. regelii and S. sewerzowii constitute a common clade with Asyneuma group, however, S. sewerzowii is more closely related to Campanula alberti (a species that has never previously been considered closely related to the genus Asyneuma or Sergia) than to S. regelii. Sergia sewerzowii is adapted to lower elevations with higher temperatures, while S. regelii prefers higher elevations with lower temperatures. The future distribution models demonstrate a dramatic loss of S. regelii range with a shift to suitable habitats in higher elevations, while the potential range of S. sewerzowii increases and shifts to the north., Conclusions: This study shows that S. regelii and S. sewerzowii have a long and independent evolution history. Sergia regelii and S. sewerzowii significantly differ in realised niches. These differences are mirrored in the response of the studied endemics to future climate warming. As suitable habitats shrink, rapid changes in distribution can lead to species' range loss, which is also directly related to declines in genetic variability. The outcomes of this paper will help to more precisely assess the impact of climate changes on rocky-related plant species found in this world's biodiversity hotspot., (© 2024. The Author(s).)