The present investigation deals with the isolation and characterization of rhizospheric diazotrophic bacteria from the rice fields of border region of India and Nepal. Molecular diversity among different isolates has been established by PCR-based techniques, restriction analysis of 16S rRNA gene, gene sequencing and DGGE. All the isolates were tested for plant growth promoting characteristics (IAA production, phosphate solubilization, and siderophore production) along with N2 fixation. A novel, rapid and simple method for the screening of IAA production plate assay technique was developed during this study. Our findings show the following significant achievements: i) novel and rapid method of detection of IAA, ii) P solubilization and ACCD activity by Microbacterium (ECI-12A), iii) Siderophore production by Agrobacterium (BN-2A) under salinity stress seems to be the first report. iv) Early flowering by inoculation of BN-2A and v) Species of Agrobacterium, Klebsiella, Serratia, Pseudomonas, Azotobacter and Microbacterium etc are predominantly present in the rhizosphere of rice plants of Indo-Nepal border region.