The recently discovered Cassia Crossbill (Loxia sinesciuris) occurs only in 2 small, isolated mountain ranges in southern Idaho, USA: the South Hills and the Albion Mountains. The species faces 2 major threats from climate change related to its reliance on seeds of Rocky Mountain lodgepole pine (Pinus contorta latifolia). First, increased numbers of hot summer days (≥32°C) since 2003 apparently caused premature cone opening and seed shedding, leading to reduced seed availability and an 80% decline in Cassia Crossbill densities between 2003 and 2011. Second, climate change is predicted to prevent recruitment and could potentially cause the extirpation of lodgepole pine from the South Hills and Albion Mountains by 2080. This extirpation would cause the extinction of Cassia Crossbills, because they are unable to compete for lodgepole pine seeds elsewhere. Although recent summers with fewer hot days have allowed Cassia Crossbills to recover, determining their status will require using density across habitat types to estimate population size. We estimated the density of Cassia Crossbills at 137 locations and used conditional modeling to evaluate the influence of 12 habitat metrics on the species' habitat use. Cassia Crossbills more commonly used larger, mature lodgepole pine stands, and north-facing slopes where cones experience less insolation and more likely retain seeds despite hot summer days. Their estimated range was 67 km² of lodgepole pine forest, with a population of ∼5,800 individuals (95% confidence interval: 3,100–11,000). Given their restricted distribution, small population, and reliance on mature lodgepole pine, the threats posed to Cassia Crossbills by climate change represent a considerable conservation challenge.