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As with other crops, loss of enough water resources especially during low falling periods is one of the main problems in rice cultivation and production in most regions of Asia. Identification of protein markers linked to drought tolerance can facilitate rice breeding process for developing new elite drought tolerant varieties. In proteome analysis of studied rice germplasm, protein was extracted from leaves of the rice plants under natural growth condition by Damerval method. Concentration of the protein samples was measured by Bradford method. Then, Two-dimensional gel electrophoresis technique was used to identify protein markers linked to drought tolerance in studied rice germplasm. Protein spots available in gel profiles of studied samples were analyzed and compared together in Melanie software. Overall, molecular data analysis of protein spots available in 2D gel profiles indicated that 20 reproducible protein spots were linked to drought tolerance in the new Iranian drought tolerant genotype.