Soil salinity is one of the major environmental factors causing crop yield loss worldwide. Different plants develop diverse salinity tolerance mechanisms to manage such a detrimental abiotic stress. The sand bean (Strophostyles helvola), a wild relative of black beans, is a native legume species and widely distributed in North America. This study focuses on understanding the molecular mechanisms of sand bean salt adaptation integrating phenotype, physiology, and genomic data. Phenotypically, beach and inland genotypes respond differently to salt treatment, and inland genotype becomes more stressed at a lower concentration of NaCl. The RNAseq based transcriptome comparisons showed the beach genotype exhibited more differentially expressed genes (DEGs) compared to the inland genotype. In addition to induced genes, constitutively expressed genes might also play important roles in sand bean adaptation to saline environments. This is a significant study to provide foundations for developing salt tolerant legume crops.