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Rice (<i>Oryza sativa</i> L.), one of the most important commodities and a primary food source worldwide, can be affected by adverse environmental factors. The chromosome segment substitution line 16 (CSSL16) of rice is considered salt-tolerant. A comparison of the transcriptomic data of the CSSL16 line under normal and salt stress conditions revealed 511 differentially expressed sequence (DEseq) genes at the seedling stage, 520 DEseq genes in the secondary leaves, and 584 DEseq genes in the flag leaves at the booting stage. Four <i>BTB</i> genes, <i>OsBTBZ1</i>, <i>OsBTBZ2</i>, <i>OsBTBN3</i>, and <i>OsBTBN7</i>, were differentially expressed under salt stress. Interestingly, only <i>OsBTBZ1</i> was differentially expressed at the seedling stage, whereas the other genes were differentially expressed at the booting stage. Based on the STRING database, <i>OsBTBZ1</i> was more closely associated with other abiotic stress-related proteins than other <i>BTB</i> genes. The highest expression of <i>OsBTBZ1</i> was observed in the sheaths of young leaves. The OsBTBZ1-GFP fusion protein was localized to the nucleus, supporting the hypothesis of a transcriptionally regulatory role for this protein. The <i>bt3 Arabidopsis</i> mutant line exhibited susceptibility to NaCl and abscisic acid (ABA) but not to mannitol. NaCl and ABA decreased the germination rate and growth of the mutant lines. Moreover, the ectopic expression of <i>OsBTBZ1</i> rescued the phenotypes of the <i>bt3</i> mutant line and enhanced the growth of wild-type <i>Arabidopsis</i> under stress conditions. These results suggest that <i>OsBTBZ1</i> is a salt-tolerant gene functioning in ABA-dependent pathways.