Researchers need continuously improve their views on mechanisms of salt tolerancein crop plants in order to overcome their limitations and improve yields understress conditions including salt stress. One of the most important methods of controllingstresses in plants is through making adjustments during the process of genetranscription. Transcription factors adjust the degree of expression in many genesby 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, andZpt2-1in salt tolerance by investigating their expression patterns under salt stress inthe leaf and root tissues of the Yazdi (salt tolerant) and the Diabloverde (sensitiveto salinity) genotypes of Alfalfa. Results showed that short-term salt stress affectson expression patterns of the CBF4, Zpt2-1, and bHLH genes in leaf and root tissuesof both genotypes. Using qRT-PCR (Real-Time PCR) analysis, it was shownthat 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 higherexpression levels of the transcription factors Zpt2-1 and CBF4 were accompaniedby greater salt tolerance. This finding can help plant breeders to use these transcriptionfactors for selecting salt-tolerant genotypes in alfalfa.