Transcripts of the Arabidopsis transcription factor gene, AtMYB44, accumulate rapidly to mediate a tolerance mechanism in response to salt stress. The AtMYB44 promoter is activated by salt stress, as illustrated in AtMYB44pro::GUS transgenic plants. Chromatin immunoprecipitation (ChIP) assays revealed that RNA polymerases were enriched on the AtMYB44 gene, especially on TSS-proximal regions, and nucleosome density was markedly reduced in the AtMYB44 gene-body region in response to salt stress. In addition, H2A.Z occupation was significantly decreased at the AtMYB44 promoter, transcription start site (TSS), and gene-body regions. Histone modifications including histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 and H4 acetylation (H3ac and H4ac) were not affected under the same stress conditions. We found a decrease in the number of AtMYB44 proteins bound to their own gene promoters in response to salt stress. These results suggest that salt stress induces the eviction of H2A.Z-containing nucleosomes from the AtMYB44 promoter region, which may weaken its affinity for binding AtMYB44 protein that acts as a repressor for AtMYB44 gene transcription under salt stress-free conditions.