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Carlina acanthifolia subsp. utzka (Hacq.) Meusel & Kästner) is one of the rarest plant species of Central and Eastern Europe and is under strict protection in this region. In view of the unfavourable tendency for the C. acanthifolia subsp. utzka population to decrease, this study attempts to assess the danger to its habitats. Polish and Ukrainian populations representing the north-western distribution limits of the species were studied. All habitat features, such as the area, number of specimens, being overgrown by trees and shrubs, or dead biomass quantity, were varied and, according to the guidelines for natural habitat monitoring, most of these parameters had an unsatisfactory index. A molecular analysis of specimens representing these habitats was performed using the ISSR (Inter Simple Sequence Repeats) method. The results of the molecular survey revealed a very low genetic diversity of C. acanthifolia subsp. utzka. Moreover, 95% of the observed genetic variability was due to variation among groups. The significant difference in the level of genetic variation was ascertained between Polish and Ukrainian populations. The lack of intrapopulation diversity indicates that the analysed populations presumably reproduce using apomixis, and rare polymorphism is the result of somatic mutations rather than facultative sexual process. This reinforces the hypothesis that unfavourable environmental and stressful conditions are natural triggers for expressing apomixis. Genetic intrapopulation uniformity makes C. acanthifolia subsp. utzka especially susceptible to climatic fluctuation. Climate changes also affect xerothermic grasslands, i.e. areas where this species occurs. In Europe, xerothermic calcareous grasslands are restricted to small extra-zonal stands and are threatened by extinction. The best method of protecting grassland areas and, consequently, C. acanthifolia subsp. utzka is the extensive grazing of mostly small ruminants. However, this method of land management cannot be used systematically. Therefore, it is necessary to investigate the causes of extinction as well as develop other effective strategies for the conservation of this rare and endangered species.