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Pinus cembra L. is a key species of high elevation forest ecosystems in Europe. However, in most mountain ranges, its importance has declined considerably. Remnant populations are often isolated and their dynamics and functioning are not well understood. Here, we apply novel approaches in pattern analysis to two P. cembra populations in the Carpathian Mountains in order to identify commonalities and divergences in their spatial structure and dynamics. Four study sites (1.2 ha each) were investigated within the treeline ecotone in two protected areas that differ in terms of protection status. Based on height and diameter, the individuals were classified into three size-classes: sapling, intermediate and adult trees. Spatial distribution and interactions between tree sizes were analyzed using point pattern analysis. The overall structure of all trees was aggregated at a small distance and regular at a greater distance in the population from the Natura 2000 site (p = 0.002), while in the National Park population it was a random pattern. However, the general patterns do not apply to tree size classes and the relationship among them. In the Natura 2000 site, there was no correlation, all the trees were mixed, regardless of their size. In the National Park, the sapling and intermediate were strongly clustered (p = 0.001), but the adult trees were spatially separated from all juveniles, forming patches at a lower elevation. In both areas, spatial patterns indicate the dynamics of the P. cembra population. Whereas in the National Park population, there is evidence of an upward shift, which cannot be confirmed in Natura 2000, where size classes are completely mixed and the dynamic does not translate into an expansion of the population area. The spatial differences between the two populations indicate that conservation strategies need to be developed more individually to support the regeneration of these isolated populations.