The results of the study of rare communities in the middle reaches of the Lena river valley, one of the most floristically rich regions of Yakutia, are presented. There are grow populations of 81 species of vascular plants listed in the regional Red Book. Populations of 35 species are covered by various types of protection. Five populations of endemic plants of the North-East of Russia, 13 species living on the northern limit of their ranges, and 3 endemic plants of the Central Yakutia were not included in protected areas (PAs). The relict steppe communities with Artemisia martjanovii Krasch. ex Poljak., Krascheninnikovia ceratoides (L.) Gueldenst., Hedysarum gmelinii Ledeb., Astragalus lenensis Shemetova, Schaulo et Lomon. are under threat of complete extinction.