Objective This paper identifies the distribution characteristics of plant diversity and phylogenetic structure types in Beijing, so as to provide a scientific basis for the conservation of biodiversity in Beijing’s natural ecosystems.

Method We incorporated phylogenetic analysis methods into floristic study, constructed phylogenetic trees of vascular plants by collecting plant catalogs, distribution information, and records from districts and various protected areas in Beijing. We calculated phylogenetic diversity and assessed taxonomic richness to identify the distribution patterns of plant diversity in Beijing. By calculating net relatedness index, we explored the phylogenetic structure of plants in various districts and multiple protected areas in Beijing. The phylogenetic similarity index Phylosor was calculated for each pair of protected areas, and cluster analysis was conducted on 14 protected areas based on both species composition similarity and phylogenetic similarity.

Result (1) The floristic composition in Beijing was complete, including all major clades of vascular plants worldwide. (2) Districts with higher altitude mountains, such as Yanqing, Mentougou, Miyun, Huairou, and Fangshan districts, exhibited higher taxonomic richness and phylogenetic diversity. (3) The taxonomic richness and phylogenetic diversity of plant genera and species in different districts and protected areas were significantly correlated, but their phylogenetic structures were non-random. Among them, Huairou District, Mentougou District, and Miyun District had overdispersed phylogenetic structure. (4) Cluster analyses based on species similarity and phylogenetic similarity were both unable to distinguish protected areas located in the Taihang Mountains and Yanshan Mountains of northern China. (5) The highest phylogenetic diversity was found in Xiaolongmen, Baihuashan, Labagoumen, and Wulingshan Mountains, among which, Wulingshan Mountains and Labagoumen had a overdispersed phylogenetic structure.

Conclusion The plant diversity hotspots in Beijing are mainly concentrated in the northern and western mountainous areas, Yanqing, Mentougou, and Miyun districts exhibite the highest plant diversity. Among the 14 protected areas, Xiaolongmen and Baihuashan Mountains exhibit the highest taxonomic richness and phylogenetic diversity, needing particular attention. Wulingshan Mountains and Labagoumen show a overdispersed phylogenetic structure, offering potential for higher conservation benefits, which should not be overlooked. Flora of Taihang and Yanshan mountains in Beijing does not exhibit significant differences.