Whitebark pine (Pinus albicaulis Engelm.) forests in western North America are increasingly threatened by the exotic pathogen white pine blister rast (Cronartium ribicola J.C. Fisch.). Whitebark pine is designated a high priority species on the candidate list of Endangered or Threatened species, spurring activity to monitor the rast infection and develop restoration strategies. We surveyed two major whitebark pine ecosystems (Northern Divide Ecosystem [NDE], including Glacier National Park, and Greater Yellowstone Ecosystem [GYE], including Yellowstone National Park) to quantify stand density, structure, species composition, blister rust infection, and mortality. We compared ecosystems based on these variables and suggest alternative restoration strategies. Overall stand densities were similar between the two ecosystems; however, NDE forests had only 79 live whitebark trees ha-1 compared to 274 in the GYE. Rust infection, crown kill, and mortality were all significantly greater in NDE forests. Nearly 75% of all whitebark trees in the NDE were dead, and approximately 90% of the remaining whitebark were infected with rust. These high infection and mortality levels suggest that planting rust-resistant whitebark seedlings should be a high-priority restoration strategy in the NDE. Conversely, nearly 30% of large seed-bearing whitebark remain uninfected in the GYE, indicating that avian seed dispersal should be reasonably dependable during good cone years in that ecosystem. Our study preceded a recent bark beetle (Dendroctonus ponderosae Hopkins) epidemic, and provides a comparison of rust-infected whitebark communities in two major ecosystems under virtually beetle-free conditions, and establishes a baseline for assessing impacts of beetles in the future.