Although mountainous habitats contribute substantially to global biodiversity, comparatively little is known about biogeographic patterns of distributions of alpine species across multiple mountain ranges. Here, we present a detailed analysis of the distributions and phylogenetic affinities of alpine seed plant lineages across North, Central, and South American mountain systems. Using a large dataset that characterizes the elevational niches of American seed plants in a continuously valued way, we related the proportion of alpine habitat occupied by plant lineages to their biogeographic distributions at a regional scale and place these results in a phylogenetic context. We found alpine species diversity to be greatest in the central Andes and western North America, and that assemblages with lower phylogenetic diversity contained species with a greater degree of alpine specialization. In particular, near-Arctic/boreal alpine communities were characterized by low phylogenetic diversity and higher degrees of alpine specialization, whereas the opposite was observed for southern Patagonian communities. These results suggest that abiotic filtering alone in these climatically similar regions is unlikely to explain alpine community assembly. Nevertheless, the overall relative rarity of alpine specialists, and the tendency for such specialists to be most closely related to montane lineages, suggested that filtering was still an important factor in shaping alpine community structure. This work corroborates the importance of a nuanced and scale-dependent perspective on the ‘history-filtering’ debate axis, as both factors have likely contributed to modern biodiversity patterns observed in alpine plant communities across the Americas.