Plants respond differently to salinity stress due to their unique gene architectures. Among genes, transcription factors (TFs) regulate many physiological and biochemical processes by modulating the rate of transcription initiation of target genes. Modulation of TFs has been correlated to the salt adaptation of any given genotype. In order to identify the expression of eight TFs (belong to bHLH, CBF, MYB, WRKY, and Zpt2 families) in three annual Medicago genotypes (M. polymorpha cv. Ieze, M. laciniata cv. Shushtar, and M. laciniata cv. Gheshm) under salinity stress, the RT-qPCR analyses were performed. Attempts were also made to establish relationships between gene expression profiles and morpho-physiological traits in these genotypes. In response to salinity, cv. Ieze had minimal changes in biomass, the electrolyte leakage, H₂O₂ content, and the higher ratio of reduced to oxidized glutathione than the other genotypes. Furthermore, Ieze had lower accumulation of Na⁺ and less decrease in K⁺ content. Altogether, it is concluded that Ieze could be regarded as a salt tolerant genotype. Transcriptome profile showed considerable variation across Medicago genotypes and among plant tissues. Among five TFs, Zpt2-2 and CBF4 had higher expression in salt-tolerant genotypes suggesting these genes as good candidates in genetic improvement programs to produce stress-tolerant plants.