The study of intraspecific variability of rare plants allows to estimate the level of phenotypical variability, to establish borders of populations, to characterize microevolutionary processes, to reveal the ecological factors influencing formation of structure of populations that finally promotes preservation of a gene pool of rare species. Work purpose: studying of intraspecific variability of rare species Iris pumila L. in the south of the Cis-Urals of Bashkortostan Republic.