The diversity of endophytic bacteria in the sand-fixation plant Caragana microphylla was investigated by amplified rDNA restriction analysis and by sequence and phylogenetic comparisons of the 16S rRNA genes. A total of 24, 19, and 17 operational taxonomic units were identified from 16S rDNA libraries of the plant roots, stems and leaves, respectively. Homology analysis revealed a 92-100% identity of bacterial 16S rDNA sequences compared with those in the GenBank database. The bacteria identified by sequence homology fell into the following groups: α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, bacilli, and uncultured bacterium. Sequence analysis demonstrated that the roots were colonized predominantly by Bradyrhizobiaceae, while bacteria from Burkholderiaceae and Sphingomonadaceae were predominant in the stems and leaves, respectively. Additionally, the endophytic bacterial community in leaves was more diverse than those in the roots and stems. Overall, the most abundant bacteria in all three tissues analyzed were from the Sphingomonadaceae and Burkholderiaceae families, although many bacterial populations were found in only a single tissue. These results suggest that the bacterial population of C. microphylla is diverse.