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Soil salinity is a major limiting factor for crop productivity, which increases continuously due to climate change. This barrier can possibly be overcome with the occurrence of halotolerant endophytic bacteria which reportedly plays an important role in protecting plants against various environmental stresses. Therefore, plant growth-promoting microbes are used in agriculture as an inexpensive and eco-friendly technology to enhance crop productivity in saline areas. In this study, the three isolates with nitrogen fixation ability were applied for mitigation of salt stress. The isolates were coded as C3A1, C8D2, and K10P4 and applied to rice plants by seed priming method. Furthermore, they were given as single innoculant or combined as a consortium compared to control, which was without the addition of endophytic bacteria, while the inoculated seed was planted on saline semisolid Fahraeus media at 4 dS m−1. The results showed that the single isolate of K10P4 endophytic bacteria increased the dry weight of rice plants, N uptake, and chlorophyll of plants in saline conditions. The combination of K10P4 isolate with C8D2 was synergistic and increased the population of endophytic bacteria in root tissue and chlorophyll content compared to the combination of C3A1 or three isolates. Meanwhile, the use of the 16S ribosomal RNA method on C3A1, C8D2, and K10P4 indentified the isolates as Ochrobactrum tritici (C3A1), Pseudomonas stutzeri (C8D2), and Pseudomonas stutzeri (K10P4).