Central Pamir-Alai, which is located almost entirely within the area of Tajikistan, is one of the world hotspots of biodiversity, harbouring ca. 4,300 species and 1,400 endemic plants. The first application of the IUCN Red List criteria reveals that among all native species occurring in Tajikistan 1,627 taxa (38.11%) are threatened, including 23 extinct (0.54%), 271 (6.34%) critically endangered (CR), 717 (16.79%) endangered (EN) and 639 (14.96%) vulnerable (VU). Globally, 20 taxa are extinct, 711 (16.65%) threatened, including 144 (3.37%) critically endangered, 322 (7.54%) endangered and 245 (5.73%) vulnerable. As we found positive correlation between human density and the number of threatened species, we suspect this indirect factor responsible for the species diversity decline. Extinct or threatened taxa have short blooming periods in spring or early summer, have limited geographical range and inhabit mainly valley bottoms at lower altitudes. Threatened taxa occupy extremely dry or wet habitats, such as deserts, semi-deserts, water reservoirs and fens. The group of threatened plants consists mostly of Central Asian, Indo-Indochinese and Arctic species. Ornamental plants have a higher extinction risk than other plants, but species collected for medicinal reasons and used for forage or food reveal lower retreatment rate. Our assessment fills a gap for important plant area and provides the data for raising the effectiveness of plant diversity conservation.