Excess salinity is one of the major abiotic stresses that plants face due to environmental changes which have multifaceted detrimental consequences including growth inhibition, disease progression and toxic metabolites production. In nature, several microorganisms can potentially reduce or alleviate salinity stress to plants through a symbiotic relation by modulating many plant physiological processes. Measuring the gene expression level in plants while having this microbe-plant symbiosis can provide us insights regarding microbial effects on plant salt stress tolerance. In this research, we used soybean ( Glycine max) seeds with and without BiostartRTM (Bio-Cat Microbials, Shakopee, MN through Rincon-Vitova Insectaries Inc., Ventura, CA) microbial inoculants to study plant gene expression during salinity stress. We germinated seeds with and without BiostartRTM in either 0 or 70 mM salt concentrations. After harvesting the leaves, we isolated the RNA, performed qPCR and analyzed the gene expression data. We observed both up-regulation and down-regulation in the expression of defense, anti-oxidant, pathogenesis, heat shock, and photosynthesis related genes. Although we did not observe any specific pattern in the expression level of these genes, genes like polyphenol oxidases, protease inhibitor, lipoxygenase, glutathione-S-transferase were significantly unregulated, several other genes such as RuBisCO, dehydrin, Aquaporin was down-regulated. The gene expression study reflects how these microbial inoculates affects soybean salt tolerance by modulating its gene expression, sometimes, by up-regulation or by suppression various plant genes.