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Climate changes and anthropogenic factors are the main factors contributing to the destruction of natural ecosystems. The aim of this study was to investigate the extent to which wild plants adapt to UV, gamma background, and gross beta activity, as well as the possible damage that can be recorded in plants growing at different altitudes in Rila Mountain. We used physicochemical, cytogenetic, and molecular methods. Our investigations were done on the nine plant species characteristic of the ecosystems in Rila Mountain at three altitudes: 1500m, 1782m, and 2925m. The registered beta activity in the plants did not depend on the altitude of the habitats. Our results showed that wild plant species differ in their tolerance to the combined effect of UV and IR radiation as well as climate factors. The genotype plays a more important role than the difference in the habitat altitude. The comet assay adapted by us for these plant species showed that the DNA of Epilobium angustifolium L. (Onagraceae) growing at 1500m was more susceptible to damage than that of Dactylis glomerata L. (Poaceae). Both these species growing at 1782m did not show any increase in DNA damage evaluated as the level of DNA migration. The level of DNA damage in Pedicularis orthantha Griseb. (Orobanchaceae) at 2925m was comparable to that at a lower altitude. Regarding the formation of micronuclei, grass species were more sensitive to UV- and IR-induced DNA damage than cereals. Our data imply the existence of specific protective mechanisms developed by plants to overcome DNA damage induced by stress factors.