Abstract: Legume, with a strong resistance to the adverse environmental conditions, is one of pioneer plants in the desert region and plays an important role in the protection of the ecological environment. In this study, the symbiosis of rhizobia associating with shrubby and herbaceous legumes in Shenmu area, Shaanxi, China was characterized by the 16S rRNA PCR-RFLP and sequence analysis of involved genes. A total of 55 strains were isolated and purified, including 30 strains from the shrubby legume Amorpha fruticosa and Caragana microphylla, and 25 strains from herbaceous plants Astragalus adsurgens, Medicago sativa and Astragalus melilotoides. Results showed that there were 11 16S rRNA genotypes. The strains isolated from herbaceous legumes belonged to five genus including Mesorhizobium, Ensifer, Rhizobium, Phyllobacterium and Agrobacterium, which were very close related to M. huakuii, M. mediterraneum, M. robiniae, E. fredii, E. meliloti, R. indigoferae, R. radiobacter, P. ifriqiyense and Ag. tumefaciens through the phylogenetic analysis. The strains isolated from shrubby legumes belonged to Mesorhizobium, and they were very close related to M. huakuii and M. mediterraneum which were shared simultaneously by shrubby and herbaceous legumes. All of these indicated the choice of rhizobia by the two types of legumes in the arid area was different, and it might depend on the species of host plant and environmental factors.