Soil salinity is a critical obstacle in modern agriculture which devastates crop growth. Many plants have developed different strategies to sense, transduce, and develop tolerance to salinity. Plant adaptation to salinity stress includes complicated metabolic pathways, genes and molecular networks. Here, we used gas chromatography-mass spectrometry (GC-MS) to understand the metabolic responses of soybean seedlings upon various levels of salt stress treatments. To this end, one salt tolerant and one salt sensitive soybean cultivar, namely Dongnong 69 and Dongnong 63 were used in this study. A total of 10 metabolites, including sugars, amino acids and organic acid, were identified as differential biomarkers. Our results indicated that these biomarkers were closely related to salinity tolerance in soybean seedlings. In particular, three metabolites, namely isoleucine, serine and aspartic acid, were found respond significantly differently between the different soybean cultivars. These three metabolites can be therefore served as potential biomarkers to screen for salt tolerant soybean cultivars. Overall, results of this study help to improve our knowledge with respect to plant salt tolerance in general, and soybean in particular

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