Kazakhstan harbors the richest flora in Central Asia. However, its current plant diversity faces significant challenges. We present an updated checklist of vascular plants for Kazakhstan, comprising 6035 taxa from 134 families and 1016 genera. This includes 485 endemic taxa (8.0% of the flora) from 38 families and 147 genera, and 359 threatened taxa (6.0%) from 66 families and 203 genera. Among them, the genera with the most endangered species are Tulipa, Astragalus, and Allium. Based on the latest available data, we describe and analyze the diversity and distribution of vascular plants at a phytogeographic regional scale of 29 regions and 7 subregions. Our analyses specifically quantify patterns of species richness, phylogenetic diversity, and the spatial distribution of both threatened and endemic species. Furthermore, floristic similarity analysis revealed clear patterns of species turnover: high similarity between adjacent mountain regions and low similarity between mountains and arid western regions. Analysis revealed five key biodiversity hotspots, including the Karatau Mountains and Western Tien Shan, which host high concentrations of threatened species yet have limited protected area coverage. Our findings underscore the need to align national and international conservation assessments, expand protected area networks, and enhance cross-border collaboration. These results provide important guidance for the conservation and sustainable management of plant diversity in Kazakhstan.