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Histone acetylation and deacetylation play essential roles in eukaryotic gene regulation. HD2 (HD-tuins) proteins were previously identified as plant-specific histone deacetylases. In this study, we investigated the function of the <i>HDT1</i> gene in the formation of stem vascular tissue in <i>Arabidopsis thaliana</i>. The height and thickness of the inflorescence stems in the <i>hdt1</i> mutant was lower than that of wild-type plants. Paraffin sections showed that the cell number increased compared to the wild type, while transmission electron microscopy showed that the size of individual tracheary elements and fiber cells significantly decreased in the <i>hdt1</i> mutant. In addition, the cell wall thickness of tracheary elements and fiber cells increased. We also found that the lignin content in the stem of the <i>hdt1</i> mutants increased compared to that of the wild type. Transcriptomic data revealed that the expression levels of many biosynthetic genes related to secondary wall components, including cellulose, lignin biosynthesis, and hormone-related genes, were altered, which may lead to the altered phenotype in vascular tissue of the <i>hdt1</i> mutant. These results suggested that <i>HDT1</i> is involved in development of the vascular tissue of the stem by affecting cell proliferation and differentiation.