Salinity is a serious limiting factor for the growth of rhizobia. Some rhizobia are tolerant to salt stress and promote plant growth, but the mechanisms underlying these effects are poorly characterized. The growth responses and osmoprotectants in four Bradyrhizobium strains were examined under salt stress in this study. Two-dimensional electrophoresis (2-DE) and mass spectrometry were conducted to investigate protein profiles in rhizobia exposed to salt stress. Subsequently, salt tolerance in stylo (Stylosanthes
guianensis) inoculated with rhizobia was further detected in hydroponics. Results showed that the Bradyrhizobium strain RJS9-2 exhibited higher salt tolerance than the other three Bradyrhizobium strains. RJS9-2 was able to grow at 0.35 M NaCl treatment, while the other three Bradyrhizobium strains did not grow at 0.1 M NaCl treatment. Salt stress induced IAA production, and accumulation of proline, betaine, ectoine, and trehalose was observed in RJS9-2 but not in PN13-1. Proteomics analysis identified 14 proteins regulated by salt stress in RJS9-2 that were mainly related to the ABC transporter, stress response, and protein metabolism. Furthermore, under saline conditions, the nodule number, plant dry weight, and N concentration in stylo plants inoculated with RJS9-2 were higher than those in plants inoculated with PN13-1. These results suggest that the tolerance of RJS9-2 to salt stress may be achieved by the coordination of indole-3-acetic acid (IAA) production, osmoprotectant accumulation, and protein expression, thus promoting stylo growth.