Abstract: Azotobacter and Azospirillum are known as non symbiotic free living nitrogen fixing biofertilizer microorganisms which actively participate in nutrients cycles. In eastern Uttar Pradesh of India, there is a great diversity in various cropping systems that may possess variation in these important biofertilizer microorganisms. The present study was conducted in order to chalk out the diversity of Azotobacter and Azospirillum sp. in different districts of eastern Uttar Pradesh in India with respect to the prevailing cropping system. Sixty two soil samples were collected from different crop rotations namely rice-wheat, vegetables, agroforestry and grassland for enumerating the diversity of Azotobacter and Azospirillum. The result showed that the Azotobacter population in rice-wheat, vegetables, agroforestry and grassland based crop rotations varied from 10x105 -13x105, 12x105-16.5x105, 9x105-15.5x105 and 7x105-10.5x105 CFU g-1 soil, respectively. Population of Azospirillum in rice-wheat, vegetables, agroforestry and grassland based crop rotations varied from 5.5x105-10.5x105, 6.5x105-12x105, 5x105-13x105 and 4.5x105-10x105 CFU g-1 soil, respectively. The diversity in population density of Azotobacter was maximum in soil of agroforestry followed by vegetables, grassland and lowest in rice-wheat based crop rotations, while in case of Azospirillum diversity was maximum in agroforestry and the lowest was observed in the rice-wheat but similar diversity present in vegetables and grassland crop rotations soil of eastern Uttar Pradesh. Overall maximum diversity of both the biofertilizer micro-organisms occurred in agroforestry based crop rotation.