Nature reserves are one of the most important measures in saving biodiversity, however, during the climate change, a real danger arises, that these territories would not be able to fulfill the objectives. In order to mitigate negative effects of climate change in protected areas it is necessary to create and apply management programs, based on future ecosystems needs. The main aim of presented study was to evaluate sensitivity of rare and vulnerable species to climate change in order to suggest measures for better management of nature reserves in the future. According to scientific literature, 12 biological and ecological plant characteristics determining sensitivity of species (limiting factors) have been detected. 73 plant species that are protected in Lithuanian reserves were evaluated qualitatively according to limiting factors of climate change. As the result, it was offered to apply additional protection measures to 47 species in the light of climate change. Groups of plant species that should be affected highly negatively or highly positively were identified. 16% of plant species protected in nature reserves were evaluated as very sensitive to climate change and the condition of these plants may worsen. On the other hand, 14 plant species were given as least sensitive to negative effects and future climate is more favorable to species growth and spread than the existing. The highest danger is predicted for Silene chlorantha (Willd.) Ehrh., and the best condition is predicted for Mentha longifolia (L.) Huds. Dactylorhiza incarnata (L.) Soó. The study also gives recommendations for the protection of rare plants in the future. Different management measures are taken into account: mitigation of the direct effect of climate change (I), improvement of an existing level of rareness (II), respecting the relation to physical and biological environment (III), consideration of spread and geographical limits (IV). Three management intensity levels were suggested according to species sensitivity.