Whitebark pine (Pinus albicaulis) (PIAL) is a proposed threatened species that plays a keystone ecological role in the Greater Yellowstone Ecosystem (GYE). Its population response to climate change is of high interest to managers because climate-induced declines may adversely affect critical ecosystem services that this species provides. While previous studies of reproductive size classes of the species have projected dramatic reductions in area of suitable habitat under climate warming scenarios, it has been suggested that the species can tolerate warmer and drier conditions if seedlings and saplings are not competitively excluded by other conifer species. Thus, we asked if juvenile-sized PIAL are found in warmer and drier locations than larger individuals, under the assumption that competitive exclusion would require several years to decades to influence the distribution of regenerating PIAL. We used a new genetic technique to distinguish non-cone bearing PIAL from the more warm-dry tolerant limber pine (P. flexilis) among samples collected along transects extending from lower treeline to the subalpine around the GYE. Predictor data on climate and water balance were obtained from a 250-m spatially explicit data product. We used a stochastic gradient boosting model to predict probability of presence of PIAL < 1 cm dbh (diameter at breast height) and >=1 cm dbh as a function of these predictors. We discovered that smaller diameter PIAL were not proportionally more abundant at lower elevations, suggesting that competitive exclusion may not be the primary mechanism limiting this species' low elevation distribution. In contrast, the small size class PIAL were slightly less warm-dry tolerant than larger individuals. This suggests that the zone of regeneration of PIAL has shifted upwards in elevation in recent decades, perhaps associated with the observed warming in the GYE. In comparison to a previous study of reproductive-sized trees (>20 cm dbh) from a coarser (1.6 km) sampling frame, however, the predicted zone of suitable habitat of PIAL (<1 cm dbh) was 122 m lower in elevation. We conclude that consideration of the fine-scale distribution of PIAL near lower treeline suggests that the tree species is slightly less sensitive to climate warming than found by previous studies of reproductive-sized trees, but, nonetheless, large range contractions of PIAL in GYE are likely under projected future climates.