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In the era of anthropocene, global warming tends to alter the distribution range of the plant species. Highly fragile to such changes are the species that are endemic, inhabit higher elevations and show narrow distribution ranges. Predicting and plotting the appropriate suitable habitats and keeping knowledge of how climate change will affect future distribution become imperative for designing effective conservation strategies. In the current study we have used BIOMOD ensemble forecasting to study the current and predict the future potential distribution of Dactylorhiza hatagirea and Rheum webbianum and describe their niche dynamics in Himalayan biodiversity hotspots under climate change scenarios using ecospat R package. Results reveal sufficient internal evaluation metrics with area under curve (AUC) and true skill statistic (TSS) values greater than 0.8 i.e. 0.93 and 0.98 and 0.82 and 0.90 for D. hatageria and R. webbianum respectively, which signifies robustness of the model. Among different bioclimatic variables, bio_1, bio_3, bio_8, bio_14 and bio_15 were the most influential, showing greater impact on the potential distribution of these plant species. Range change analysis showed that both the studied species will show significant contraction of their suitable habitats under future climatic scenarios. Representative Concentration Pathway (RCP) 8.5 for the year 2070, indicate that the suitable habitats could be reduced by about 51.41% and 70.57% for D. hatagirea and R. webbianum respectively. The results of the niche comparisons between the current and future climatic scenarios showed moderate level of niche overlap for all the pairs with D. hatageria showing 61% overlap for current vs. RCP4.5 2050 and R. webbianum reflects 68% overlap for current vs. RCP4.5 2050. Furthermore, the PCA analysis revealed that climatic conditions for both the species vary significantly between current and future scenarios. The similarity and equivalence test showed that the niche between present and future climate change scenarios is comparable but not identical. From the current study we concluded that the influence of climate change on the habitat distribution of these plant species in the Himalayan biodiversity hotspots can be considered very severe. Drastic reduction in overall habitat suitability poses a high risk of species extinction and thereby threatens to alter the functions and services of these fragile ecosystems. Present results can be used by conservationists for mitigating the biodiversity decline and exploring undocumented populations on one hand and by policymakers in implementing the policy of conservation of species by launching species recovery programmes in future on the other. The outcomes of this study can contribute substantially to understand the consequences of climate change in the Himalayan biodiversity hotspots. [ABSTRACT FROM AUTHOR]