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Cluster bean [Cyamopsis tetragonoloba (L.) Taub, 2n=14] is an important self-pollinated legume crop. In Rajasthan it has become very popular crop in last decade. Cluster bean nodulating bacteria are highly specific for their host plant. As these bacteria do not show any serological cross- reaction with known rhizobia species, they are unique. The present investigation was carried out by isolating bacteria nodulating cluster bean from the areas of arid and semi-arid regions of Rajasthan to identify effective and competitive strains tolerant to various abiotic stresses such as temperature, pH and salinity. A total of 15 rhizobium isolates from cluster bean nodules were characterized on the basis of cultural analysis and screened for physiological traits. Most isolates were tolerant to pH between 6.0 to 8.0, NaCl concentration between 0.5 to 3% and temperature between 37 to 42 degrees C. These rhizobial isolates were characterized by random amplified polymorphic DNA to estimate their relationship on molecular basis and compared with their tolerance to various abiotic stresses. The rhizobial isolates from hot climatic area are having more tolerance to abiotic stress specially temperature, among these few rhizobial isolates which are genetically similar, also are less tolerance to abiotic stress and grouped in same cluster on the dendogram.