Beneficial aspects of endophytic microorganisms have motivated researchers to explore plant endophytic world. The present study was aimed to isolate and characterize the seed-borne endophytic bacteria from diverse maize genotypes. Eighty maize seed endophytic bacteria (MSEB), isolated from 30 maize genotypes, were characterized using polyphasic approach. The dendrograms and phylogenetic tree generated on the basis of ARDRA analysis and metabolic profiling of endophytic bacteria revealed genotypic and biochemical diversity among MSEB. The 16S rDNA sequence analysis revealed Bacillus as the most dominant encountered genus affiliated with Phylum Firmicutes. Few isolates belonged to genus Staphylococcus, whereas one isolate was identified as Corynebacterium sp. under Phylum Actinobacteria. Majority of the MSEB isolates exhibited antagonism against phytopathogenic fungi, production of ammonia, and secretion of lytic enzymes; some isolates also exhibited indole acetic acid production, the traits of which can be helpful in endophytic establishment and advantageous to the host plant. Besides, many MSEB exhibited tolerance to salinity (10%), osmotic stress (40% PEG6000), and temperature (60 °C), indicating their possible application under stress conditions. Endophytic nature of the selected MSEB isolates was confirmed by tracking their presence in shoots, leaves, and roots of the host seedlings with the help of biochemical marker (rifampicin resistance). Thus, the MSEB identified in the present study can be explored as potential bioinputs for improving plant growth and productivity under stressed conditions, besides helping in understanding the plant-endophyte interactions.