Aim This study aimed to investigate the distribution patterns of plant diversity in Kenya, how climatic fluctuations and orogeny shaped them, and the formation of its β‐diversity. Location Kenya, East Africa. Taxon Angiosperms. Methods We quantified patterns of turnover and nestedness components of phylogenetic β‐diversity for angiosperm species among neighbouring sites using a well‐resolved phylogenetic tree and extensive distribution records from public databases and other published sources. We applied clustering methods to delineate biota based on pairwise similarities among multiple sites and used a random assembly null model to assess the effects of species abundance distribution on phylogenetic β‐diversity. Results The phylogenetic turnover of the Kenyan flora, intersecting with the biodiversity hotspots Eastern Afromontane, Coastal Forests of Eastern Africa, and Horn of Africa, shows a non‐monotonic pattern along a latitudinal gradient that is strongly structured into volcanic and coastal areas. The other areas are mainly dominated by phylogenetic nestedness, even in the eastern part of the equatorial region parallel to the volcanic area. Phylogenetic diversity and phylogenetic structure analyses explain the mechanism of the observed phylogenetic turnover and nestedness patterns. We identified five phytogeographical regions in Kenya: the Mandera, Turkana, Volcanic, Pan Coastal and West Highland Regions. Conclusions Variations in turnover gradient and coexistence are highly dependent on the regional biogeographical history resulting from climatic fluctuations and long‐lasting orogeny, which jointly shaped the biodiversity patterns of the Kenyan flora. The nestedness component dominated climatically unstable regions and is presumed to have been caused by heavy local species extinction and recolonization from the Volcanic Region. The high turnover component in climatically stable regions may have preserved old lineages and the prevalence of endemic species within narrow ranges.