Rhamnus erythroxyloides subsp. sintenisii (Rech.f.) Mabb. is a relict species occurring on the remnant mountains of Kyzylkum (in Uzbekistan). Up until recently, its population status and exact distribution remained unassessed. The ecological distribution and population status of four populations of Rh. erythroxyloides subsp. sintenisii were studied. The study of its morpho-anatomical structure revealed that the studied taxon’s vegetative and generative organs demonstrate clear adaptive features to arid climate. We observed an absence of the young fraction (seedlings and juvenile plants) in the populations, which is related to irregularity of seed renewal. Furthermore, population fragmentation due to a high degree of soil salinity and the presence of organic matter has been noticed at the present stage. According to the combination of threatening factors, the current state of the population of Rh. erythroxyloides subsp. sintenisii in Uzbekistan has been estimated as disappearing (EN)—B2ab (ii, iii, iv) + C1 + E.