The selection of salinity tolerant bacteria may provide greater promotion of plant growth in soils with salt stress. This study aimed to isolate and select bacterial isolates of sugarcane, tolerant to salinity and plant growth promoters, and assess genetic diversity. To do so, endophytic root and rhizosphere of sugarcane, were isolated in culture medium with and without NaCl. The bacterial population density, the potential for biological nitrogen fixation (BNF), production of indole acetic acid (IAA), inorganic phosphate solubilization and quorum sensing molecule production were evaluated. Furthermore, the genetic diversity was assessed by Denaturing Gradient Gel Electrophoresis (DGGE) of nifH. Salinity tolerance tests were also conducted. There was no statistical difference in population density. As for the potential for BNF, IAA production, phosphate solubilization and quorum sensing molecule production, there was a high percentage of positive isolates. In the technique of DGGE nifH, the dendrogram showed high genetic variability. So there was the selection of bacteria that can contribute to the better development of sugarcane in saline soils.