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Climate change is threatening species and habitats. Altitudinal shifts uphill and negative population trends are commonly observed in altitude-related taxa. The bumblebee Bombus alpinus (Linnaeus, 1758) has a disjoint distribution restricted to Fennoscandia and the Alps, and is considered threatened. We studied the ecology and distribution of B. alpinus in the Alps, where the endemic subspecies Bombus alpinus helleri Dalla Torre 1882 is found, as a case-model because of its rarity, habitat, and mutual dependence with the ecosystem for pollination and resources. We developed species distribution models including both climatic and habitat variables to obtain the surface suitable for this subspecies and quantified its protected portion. Our analyses indicate that this bumblebee is restricted to the upper altitudes and has a narrow niche mainly related to the presence of glaciers, the cool temperature, a low temperature variation, and a specific range of precipitation. A strong altitudinal shift is also taking place probably due to climate change. After years of no changes in altitudinal distribution, its lowest altitudinal limit has moved up 479 m since the year 1984, while its upper altitudinal limit has remained unchanged. Over half of the suitable area in the Alps is included within protected areas, but conservation has not been planned yet. However, rare species with narrow niche, such as B. alpinus, are highly threatened by climate change. Potential short-term mitigation actions are discussed, including exchange of males between locations and integral protection of prairies in the vicinity of glaciers.