The páramo ecoregion is known for its remarkable biodiversity and evolutionary histories shaped by complex biogeographical processes. To protect and conserve the ecological diversity and evolutionary lineages in this hotspot requires analyzing spatial patterns of phylogenetic diversity and endemism. This study uses spatial phylogenetic methods, combining georeferenced occurrence data with a genus-level phylogeny of the region’s entire vascular flora to investigate the spatial distributions of phylogenetic diversity and endemism. In this study, we assembled a comprehensive dataset of 361 equal-area grid cells covering the páramo biome and compiled occurrence records for 567 vascular plant genera. A phylogeny of vascular plants in the páramo was generated by combining publicly available genetic sequence data with novel genetic data from Colombian herbarium collections. This study examined the vascular plant diversity in the páramo ecosystem and identified distinct centers of neo- and paleoendemism, as well as a strong pattern of phylogenetic clustering across most páramo regions. The phylogenetic beta diversity analysis identified several phylogenetically distinct bioregions, characterized by both widespread, shared evolutionary histories and localized, distinct assemblages. This study provides a scope to prioritize certain areas for protection and to further identify and understand biogeographical patterns in the páramo ecoregion. The dataset provided here is an alignment of 5 chloroplast DNA marker sequences aiming to represent all á vascular plant genera.