[Objective] in order to screen and identify endophytic bacteria with nitrogen fixation and pathogen inhibition functions, 21 endophytic bacteria were isolated from Polygonum viviparum on the Eastern Qilian Mountains in the Qinghai-Tibetan Plateau, China. [Methods] Nitrogen fixation endophytic bacteria were identified by the 16S rRNA genes sequences analysis, physiological and biochemical characterization. [Results] The results show that 28.6% endophytic bacteria of Polygonum viviparum could fix nitrogen and 76.2% had strong antagonistic against plant pathogen, furthermore, 23.8% endophytic bacteria inhibited more than 5 plant pathogen. Strain Z19 had strong ability of nitrogen fixation and decomposing-cellulose. The cellulase activity was 0.31 U, and ratio of the diameter of lysis zone to colony diameter was up to 3.33. Furthermore, strain Z19 inhibited pathogenic fungi, such as Rhizoctonia solani, Sclerotinia sclerotiorum, Botrytis cinerea, Bipolaris sorokiniana and Alternaria solani. Through PCR amplification and sequencing, the sequence of nifH gene and 16S rRNA gene were obtained and they were registered in GenBank (accession numbers were EU693340 and EU236746, respectively). Strain Z19 is rod, Gram-positive, and produce spore. Based on the physiological and biochemical characteristics and 16S rRNA gene sequence analysis, Z19 was identified as Bacillus subtilis. [Conclusion] The study provides new insights for the exploration and utilization of promoting growth and antagonistic endophytic bacteria in alpine grassland.