Endophytic bacteria can be defined as those bacteria that can colonize the internal tissue of a plant without causing negative effects on their host. Many endophytes can be used as agents for stimulating plant growth, and for producing bioactive natural compounds as a potential source of novel products for use in medicine, agriculture, and industry. Therefore, the study of plant endophytic bacteria is important for understanding ecological interactions and for the development of biotechnological applications. We studied the diversity, distribution, and stress resistance of endophytic bacteria isolated from Caragana microphylla, a perennial leguminous shrub that is highly tolerant to drought, salt, and extreme cold environment, from desert grassland in Ningxia, China. A total of 78 bacterial strains were isolated, and the quantity and community composition of endophytic bacteria in various tissues of C. microphylla were found to be markedly different. The bacteria colonizing in the roots was greater than that of other tissues (40 strains), followed by leaves (20 strains). The genetic diversity and phylogenetic position of the isolates were analyzed using restriction fragment length polymorphisms (RFLP) and sequence homology comparisons of the 16S rDNA gene. The isolates were classified into 11 types on the basis of PCR-RFLP results, and strains were determined to belong to six genera from five families based on 16S rDNA sequence analysis. The endophytic bacterial population of C. microphylla was found to be less diverse than that of other plants, and colonized predominantly by Bacillus species (87.2%), which were distributed in all tissues of the plant. The bacterial populations in the roots consisted of Bacillus (89.6%) and Paenibacillus, which included isolates belonging to rDNA types 1-6. The bacterial populations found in leaf tissue consisted of Bacillus and Ralstonia species, while bacteria found in the stems were mainly Bacillus, Pseudomonas, and Sinorhizobium species. Bacillus, Pseudomonas, and Cupriavidus species were isolated from seeds. Tests for stress resistance revealed that most of the isolates could tolerate NaCl stress at 6% concentration, and could grow at an initial pH of 5.0-11.0 and at a temperature of 10-45℃. A small number of isolates could tolerate NaCl stress at 10% concentration, and could grow at pH 12.0 at a temperature of 55℃. None of the isolates could grow below pH 4.0 and at a temperature of 4℃. The stress resistance of endophytic bacteria was different in various tissues, and root bacteria showed greater levels of resistance than strains isolated from other tissues. However in general, the endophytic bacteria of C. microphylla had a strong resistance capacity, among which, three strains of Bacillus were most resistant. The results of this study not only offer new information about the C. microphylla endophytes under extreme environmental conditions, but also add to our knowledge regarding the protection and utilization of microbial resources in arid areas during the management of desertification.