Comparative RAPD-analysis of DNA of Syrian bean-caper (Zygophyllum fabago), common reed (Phragmites australis) and oleaster (Eleagnus caspica) subjected to radiation and plants grown under natural background radiation was performed. Amplification of genomic DNA sample of Zygophyllum fabago using OPC-08 primer caused an increase in the band intensity at 1700 bp. At the same time, locus amplified at 520 bp in the control sample, was not revealed during the stress. As a result of the analysis, using ОРС-08, OPH14 и ОРН-01 primers, amplification of the new specific loci in Phragmites australis was observed at 1200 bp (OPC-08), 850 bp (OPH -14) and 700 bp ( OPH-01). In Eleagnus caspica new spesific locus was detected at 660 bp when using OPC-08 primer. The decrease of band intensity and the loss of some fragments were observed using the primers OPH-01, OPH-03 and OPH-15 in control and irradiated samples of Eleagnus caspica. Obtained results indicate that, the main changes observed in the RAPD profiles are expressed by both appearance and disappearance of some bands which are also accompanied by alterations in their intensities. These observed patterns might result from the structural rearrangements in DNA caused by different types of DNA damage.