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Soil salinity is a severe constraint on crop productivity that triggers plant salt stress response pathways. The salt stress responses are controlled by transcriptional regulatory networks that enhance plant stress tolerance by manipulating the expression of transcription factor (TFs)-encoding genes. Identifying TFs associated with salt tolerance contributes to salt-tolerant crop breeding. In this study, a comparative transcriptome analysis was performed to investigate the global gene expression of entire TFs in diploid and autotetraploid rice with different salt tolerance levels, considering NaCl stress, NaOH stress, and Na2CO3 stress. A total of 54, 54 and 55 TF families were co-expressed in diploid and tetraploid roots under three stresses, respectively. Furthermore, we investigated differentially expressed TFs (DE-TFs) based on different comparisons, and the statistical analysis indicated that the DE-TFs derived from the three types of stress were as follows: Na2CO3 (53 TF families, 1356 DE-TFs) > NaCl (19 TF families, 214 DE-TFs) > NaOH (18 TF families, 152 DE-TFs). These results imply that Na2CO3 stress induced a more obvious biological responses in the roots than the other two stresses. GO and KEGG pathway enrichment analysis of DE-TFs revealed the importance of plant hormone signal transduction and MAPK signaling pathways that may contribute to the saline–alkaline tolerance of tetraploid rice. This study provides gene resources that are valuable for exploring the regulatory mechanism of TFs involved in the saline–alkaline tolerance of polyploid rice. [ABSTRACT FROM AUTHOR]