Abstract:[Objective] This paper aimed to estimate the diversity and characterization of endophytic bacteria isolated from seed of Caragana leucophloea Pojark which good adaptability to desert. [Methods] The methods used in this study include seeds surface sterilization, seed coat and kernel separation, endophytic bacteria isolation, tolerance to pH and NaCl estimating, 16S rRNA gene sequencing and phylogenetic analyzing. [Results] With the thirty-two isolates, six and twenty-six strains were obtained from seed coat and kernel, respectively. The optimal pH for all strains that from seed coat was above pH 9.0 and the maximum was up to 14.0 for three of them, and the tolerance to salt was up to 10% NaCl for five isolates. The tolerance to pH of the strains isolated from kernel was significantly lower than that from seed coat, but there’s twelve strains could tolerant to salt up to 10% NaCl also. According to 16S rRNA gene sequences analysis, thirty strains belong to Bacillus sp. with the similarity between 95%?99%. Among them, thirteen isolates was closed to Bacillus subtilis with similarity 96%?99% and eleven was closed to Bacillus licheniformis with similarity 95%?99%. One strain belong to genus Sphingomonas sp. with the homology of 99%, and one belong to genus Escherichia sp. with the homology of 98%. [Conclusion] The results has showed that the diversity of endophytic bacteria of C. leucophloea’s kernel was higher than that of the coat, indicating their space distribution and species diversity. And we could speculate that the higher tolerance on pH and salt of the bacteria of the seed coat must have some relationship with the host environment adaptability.