A number of signaling pathways are involved in root development, but the role of histone acetylation and deacetylation in this process remains unclear. In this study, Trichostatin A (TSA), an inhibitor for histone deacetylases, was used to determine the effect of histone deacetylation on root development. The root length and the cell number in meristem were reduced by TSA. The result from marker lines suggested that the stem cell niche was disordered during the treatment. The expression levels of SCR and SHR were not altered but those of PLT1 and PLT2 were reduced by TSA. The analysis of the effect on auxin transport showed that the expression of PIN1 was mildly affected but PIN2 was dramatically reduced in the TSA treatment. The result from pDR5:GFP plants suggested that TSA alters the distribution of auxin in root meristem. In conclusion, TSA has effects on the maintenance of stem cell niche in the root of Arabisopsis, implying the important role of histone deacetylation in root development.