The research examines the impact of climate change on rare and endangered plant species within the walnut-fruit forests of southern Kyrgyzstan and the ecosystem of the Sary-Chelek Biosphere Reserve. Forests cover approximately 31% of the Earth’s land surface and harbor more than 80% of global biodiversity. However, anthropogenic pressures and unsystematic exploitation of plant resources lead to habitat degradation and population decline. Particular attention is devoted to Malus niedzwetzkyana, a critically endangered endemic species, with an assessment of its distribution, population structure, and reproductive biology. The research employed field observations, route-based surveys, GPS mapping, phenological monitoring, and soil analyses to evaluate habitat conditions and reproductive potential. Results indicate that Malus niedzwetzkyana occurs at elevations between 1241 and 2000 m, primarily within walnut-fruit forest zones. The number of seeds per fruit ranges from 4 to 15, with a germination rate of up to 96%. These findings provide essential data for the development of conservation strategies, propagation programs, and habitat management measures. The research underscores the urgent need to preserve biologically valuable species and maintain ecological balance under ongoing climate change.