In this study we examined the floristic diversity of the Sutai Khairkhan Mountain Nature Reserve in western Mongolia’s Altai Mountain range. This nature reserve area was established in 2019 and compared to nearby reserves, its flora is relatively understudied. From field surveys in 2014, 2019, and 2020, we collected about 400 herbarium specimens from various habitats and different altitudes in the reserve. We identified total of 317 taxa including 10 subspecies and three varieties of vascular plants belonging to 157 genera and 45 families. Among these, five species are nationally endemic, 27 species are endemic to Altai Mountains, and 37 species are threatened, including two critically endangered, 11 endangered, 16 vulnerable, and eight near threatened. In addition, we rediscovered Microula tibetica var. pratensis (Maxim.) W.T. Wang after 40 years. This first complete checklist of the SKMNR flora amplifies the value of protecting the diverse and threatened plants in the reserve and creates a baseline to assess future population changes.