Among the various stresses, salinity is a great threat to plants and the study of the mechanism of salt tolerance in plants is important. In one of the salt tolerance pathways in the model plant Arabidopsis, Salt Overly Sensitive 3 (SOS3) protein, which is a sensor of calcium ions and the initiator of a salt tolerance pathway, activates various processes in order to tolerate salinity by the formation of an SOS3-SOS2 complex. On the other hand, superoxide radicals that are produced in response to various stresses such as salinity are harmful to the cell and must be eliminated. How to remove superoxide radicals and protect cells from oxidative damage in salt-tolerant plants is not clear. In this study, the SOS3 protein interactions in Arabidopsis cDNA library were investigated using the Yeast Two Hybrid System (Y2HS), and double transformation of Saccharomyces cerevisiae AH109 strain with pGBT9-SOS3 and pGADT10-AtcDNA. DNA extraction was performed on four selected yeast colonies on SD-AHWL and pGADT10-AtcDNA vectors were amplified in E. coli, sequenced and compared to the Arabidopsis data bank. One of the most important interactions was found on Manganese Superoxide Dismutase 1 (MSD1). MSD1 neutralizes superoxide radicals to protect plants from oxidative damage caused by stresses. The interaction and the recruitment of MSD1 by SOS3 in the salinity resistance pathway should save the plant from oxidative trauma. Afterward, the interaction of SOS3-MSD1 was confirmed by isolation of complete MSD1 cDNA and cloning in yeast two hybrid vectors. In parallel, using a GST-Pull Down assay, it was shown that the SOS3 protein produced in bacterium from pGEX2TK-SOS3 vector directly interacted with the radio-labeled MSD1 produced from pGBKT7-MSD1. This is the first report of the interaction of salinity tolerance pathway (SOS3) with the elimination pathway of harmful superoxide ions (MSD1) that shows interaction between these molecular mechanisms.