Research Highlights: When biotic interactions such as disease alter both the seed production capacity of stands, and seedling survivorship, the relative importance of seed availability versus substrate specificity may alter future regeneration opportunities for plant populations. Background and Objectives: We investigated the importance of disease severity, seed availability, and substrate limitation to the regeneration dynamics of the endangered limber pine, Pinus flexilis, in two ecosystems with varying forest composition, and different histories of white pine blister rust infection (WPBR; Cronartium ribicola). Materials and Methods: A total of 17 stands from the montane ecoregion (Alberta, Canada) were sampled for seed production between 2007–2010, seedling density, and age structure. Model selection using an information theoretic approach compared a series of a priori models and their combinations, based on our hypotheses on the role biotic variables play in the regeneration process. Results: Despite higher rates of WPBR infection, 2.3 times more seed was available for avian dispersers in the southern ecosystem. Recent seedling regeneration did not correspond to seed production (83 versus 251 seedlings/ha, in southern versus northern ecosystems, respectively), resulting in a seven-fold difference in seed to seedling ratios between ecosystems. Models suggest that disease and vegetation cover were important factors explaining the absence of regeneration in 79.4% of the plots sampled, while basal area (BA) of live limber pine, rocky substrates, ecosystem, South aspects, and slope enhanced limber pine regeneration. Seedling age structures suggest that recent regeneration is less likely in more diseased landscapes, than it was historically (40% versus 72.8% of seedlings < 20 years old, respectively, in southern versus northern ecosystems). Conclusions: At the northern limits of limber pine’s range, seed availability does not ensure regeneration, suggesting that other environmental or biotic factors hinder regeneration. Regeneration was consistently predicted to be lower in the southern ecosystem than in the northern ecosystem, suggesting that natural regeneration and the potential for population recovery are ecosystem dependent. We recommend that monitoring recent seedlings will aid the identification of biotic and abiotic factors affecting regeneration.