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Rhizosphere soils of chickpea (Cicer aeritinum) and wheat (Triticum aestivum) were analysed for the diversity of diazotrophic microorganisms by sequencing the nifH gene. A clone library of soil DNA amplified using highly degenerated nifH primers targeting the prokaryotic nitrogenase was constructed and subsequent RFLP analysis of nifH gene from clone libraries identified 28 and 25 genotypes in chickpea and wheat rhizosphere respectively. A total of 41 nifH genotypes were identified, out of which 12 were common in both rhizosphere soils. Sequencing of 41 nifH genotypes showed similarity to the corresponding genera of diazotrophs belonging to alpha, beta, gamma and delta proteobacteria. The prominent diazotrophs were Azospirillum brasilense, Bradyrhizobium spp., Azotobacter chroococcum, Methylococcus capsulatus, M. sylvestris, Sinorhizobium meliloti and Burkholderia vietnamenesis. A. brasilense was the dominant diazotroph present in the both rhizosphere soils. S. meliloti was only present in the chickpea rhizosphere, while B. vietnamanesis and Azoarcus tolulyticus were observed only in the wheat rhizosphere. The chickpea and wheat rhizospheres were diverse in diazotrophic bacterial community, as indicated by the occurrence of the nifH genotypes.