Endophyte bacteria are now considered as biocontrol agents of plant pathogenic microorganisms. The aim of this study was to identify endophyte bacteria in potato tubers of Fontan 90, Agria, Sante,a and Jeli 89 by using 16S rRNA gene and investigate their antagonistic ability against some Soil-borne pathogens. First, potato tubers were planted in PDA and TSA medium, after sterilization with commercial cleaners to ensure any microorganisms. After sampling, three groups of potatoes with a skin thickness of 1mm were sampled successively from the outer skin towards the center of the excrescence's prominence. The layers of each type, with 1 mL sterile aquapura, were broken to pieces, and a 45 minute time was allowed in order for the bacteria excretions to go out. The extracts were surface cultured and identified by biological methods (morphological, physiological and biochemical attributes) and standard microbiology methods. The achieved antagonistic property of endophyte bacteria as compared to pathogene fungus like Fusarium oxosporum, Rhizoctonia solani, Verticillium dahlia, and pathogene bacteria like Stereptomayse scabies and Ralstonia solanacearum. The best antagonists were identified by 16S rRNA gene and comparing in the NCBI gene bank. The results showed that Bacillus subtilis, Bacillus mojavensis and Klebsiella variicola had the highest degree of inhibitory effect and was related to the 1st layer. All of the experiments were done with four repetitions. In the case of Klebsiella varicola as potato tuber endophyte, has been yet no reported, which was first extracted and isolated in this study and presented as a good antagonist against fungal and bacterial pathogens.