Expanding human pressure has reduced natural habitats globally and motivated strategies to conserve remaining natural habitats. Decisions about conservation on private lands, however, are typically made by local stakeholders who are motivated by the elements of nature they most highly value. Thus, national prioritization for conservation should be complemented by local analysis of species or habitats that most influence local landowner decisions. We demonstrate within the Greater Yellowstone Ecosystem how quantitative mapping of wildlife species that are highly valued by local residents can be integrated with indices of ecosystem integrity to prioritize private lands for conservation. We found that natural vegetation cover (NVC) comprised 81% of the private lands. Some watersheds have lost 6% of NVC since 2001 and developed lands now cover >40% of their areas. Locations high in ecological value, elk habitat, and grizzly habitat occurred in different biophysical settings. Consequently, only 2% of the NVC supports high levels of all three biodiversity measures and 26% of this area was within conservation easements. The remaining areas of high biodiversity value that are unprotected are priorities for conservation. We suggest that national-scale conservation planning will be most effective on private lands if additional within-ecoregion analyses are done on the elements of biodiversity that are most valued by local people.