Background <p>Climate change and shifting fire regimes are expected to alter tree regeneration dynamics, yet these impacts remain poorly resolved in high-elevation forests. Whitebark pine (<i>Pinus albicaulis</i>) is of particular concern as a federally threatened species experiencing severe decline due to white pine blister rust (<i>Cronartium ribicola</i>) and mountain pine beetle (<i>Dendroctonus ponderosae</i>). Using a 2 × 2 factorial design (burned vs. unburned, upper vs. lower elevation) across 10 sites in the Selway-Bitterroot Wilderness (Montana and Idaho, USA), we modeled seedling and sapling presence and abundance of whitebark pine, subalpine fir (<i>Abies lasiocarpa</i>), alpine larch (<i>Larix lyallii</i>), and Engelmann spruce (<i>Picea engelmannii</i>) as a function of fire occurrence, topography, forest structure, ground cover, burn severity, and post-fire climate. We also developed a geospatial model predicting whitebark pine juvenile presence and abundance at 10&#xa0;m resolution across the Bitterroot Range.</p> Results <p>Juvenile presence and abundance were often more strongly linked to biophysical site characteristics than disturbance history. Fire was associated with reduced whitebark pine sapling presence and seedling abundance but increased alpine larch seedling presence and sapling abundance. Elevation was a dominant topographic predictor, with probability of presence and abundance for both whitebark pine and alpine larch increasing at higher elevations, while subalpine fir decreased with elevation except in burned stands or where conspecific adult density was high. Burn severity effects were mediated by topography: higher severity benefited whitebark pine on warmer aspects and ridgelines, while subalpine fir abundance responded positively to higher severity only in cooler, wetter sites. Geospatial modeling indicated that conditions supporting whitebark pine juvenile presence and abundance occur in greater proportion within the Selway-Bitterroot Wilderness than in adjacent non-wilderness.</p> Conclusions <p>Juvenile tree populations in the high-elevation forests of the Bitterroot Range are shaped primarily by biophysical site characteristics and species-specific regeneration niches, with fire acting as a context-dependent modifier rather than a primary driver. For the threatened whitebark pine, we observed fewer seedlings and saplings in burned areas, likely reflecting seed source limitations stemming from the loss of cone-bearing trees over recent decades. Where seed sources are limited, planting of rust-resistant seedlings is likely necessary to restore whitebark pine populations, with priority given to sites where abiotic conditions currently favor recruitment and climate is projected to remain suitable in the long term. The spatial predictions developed here provide a practical first-pass tool for identifying such priority sites, supporting targeted monitoring and restoration planning for this keystone species.</p>