The yield of soybean is substantially reduced when the crop is grown in salinity-affected soil. This review summarizes the progress achieved in defining the genetic basis of salinity tolerance. Both forward (uncovering the genetic basis of a phenotype by exploiting natural or induced mutations) and reverse (defining the phenotype which arises as a result of an altered DNA sequence) genetics methods have been used to reveal the function of key salinity response genes. Quantitative trait locus analysis has identified six regions of the genome which harbor loci influencing salinity tolerance, and positional cloning has succeeded in isolating one important salt tolerant gene. Meanwhile the application of the genome-wide association study technique has led to the isolation of a second gene involved in salinity tolerance. Reverse genetics experiments have highlighted a number of salinity response genes, mainly including ion transporter genes and transcription factor genes. These studies lay the foundations for understanding the mechanistic basis of salinity tolerance in soybean, knowledge of which would be essential to enable the breeding of highly salinity tolerant soybean cultivars through the use of marker-assisted selection or transgenesis.