Researchers need continuously improve their views on mechanisms of salt tolerance in crop plants in order to overcome their limitations and improve yields under stress conditions including salt stress. One of the most important methods of controlling stresses in plants is through making adjustments during the process of gene transcription. Transcription factors adjust the degree of expression in many genes by binding to DNA and are thus very important in salt tolerance of plants. Therefore, the present research studied the role of transcription factors bHLH, CBF4, and Zpt2-1in salt tolerance by investigating their expression patterns under salt stress in the leaf and root tissues of the Yazdi (salt tolerant) and the Diabloverde (sensitive to salinity) genotypes of Alfalfa. Results showed that short-term salt stress affects on expression patterns of the CBF4, Zpt2-1, and bHLH genes in leaf and root tissues of both genotypes. Using qRT-PCR (Real-Time PCR) analysis, it was shown that the transcription factors Zpt2-1 and CBF4 in the salt tolerant genotype (Yazdi) were expressed at a higher level in root tissues. In other words, it seems that higher expression levels of the transcription factors Zpt2-1 and CBF4 were accompanied by greater salt tolerance. This finding can help plant breeders to use these transcription factors for selecting salt-tolerant genotypes in alfalfa.