We assessed the vulnerability of ecological processes and vegetation to climate change in the US Northern Rocky Mountains with a focus on the Greater Yellowstone Ecosystem. We found that climate has warmed substantially since 1900 while precipitation has increased. An index of aridity decreased until about 1980 and then increased slightly. Projected future climate indicates warming of about 3-7 degrees C by 2100 and a substantial increase in aridity, depending on climate scenario. Snow pack, soil moisture, runoff, and primary productivity are projected to decrease dramatically in summer under future climate scenarios, with snow pack and runoff declining annually. Habitat suitability for the four subalpine tree species is projected to contract dramatically while mid elevation tree species are projected to expand in area of suitable habitat. Across Greater Yellowstone, sagebrush communities are projected to expand and total forest cover is projected to decrease. The most vulnerable tree species are Whitebark pine and Mountain hemlock (found on the west-slope of the Rockies), both of which are projected to have 0-10% of current area of suitable habitat by 2100. These results represent the first comprehensive climate vulnerability assessment for the Northern Rockies and provide critical information for guiding the development and evaluation of climate adaptation strategies.