Mountain vipers of the genus Montivipera, generally, and the species of the Raddei clade, specifically, are interesting examples of species neo-endemism in Iran, Anatolia, and the Caucasus. Given the critical conservation status of these species, it is necessary to identify their suitable habitats for prioritizing conservation measures. We modeled ecological niche of each species based on four species distribution models, including generalized linear models, generalized boosting models, random forest, and maximum entropy and combined them in an ensemble model. Also, using a new principal component analysis (PCA-env), the ecological niche divergence of the species was investigated. Results indicated that all models with AUC and TSS > 0.9 had excellent predictive performance. The species of the Raddei clade showed different patterns of ecological niche occupation and the greatest differentiation was seen in the gradient of temperature seasonality, annual precipitation, and topographical ruggedness. M. latifii and M. kuhrangica, despite the great geographical distance, revealed the highest degree of niche overlap and niche similarity. Due to the restricted distribution and limited evolutionary adaptability of mountain vipers in the mountainous regions of Alborz and Zagros, it is imperative to plan conservation measures to reduce the factors that threaten the long-term survival of these species.