Histone acetylation, which is an important mechanism to regulate gene expression, is controlled by the opposing action of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In animals, several HDACs are subjected to regulation by nitric oxide (NO), in plants however, it is unknown whether NO affects histone acetylation. We found that treatment with the physiological NO-donor S-nitroso-glutathione (GSNO) increased the abundance of several histone acetylation marks in Arabidopsis, which was strongly diminished in the presence of the NO scavenger 2-4-carboxyphenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO). This increase was likely triggered by NO-dependent inhibition of HDAC activity since GSNO and S-nitroso-N-acetyl-DL-penicillamine (SNAP) significantly and reversibly reduced total HDAC activity in vitro (in nuclear extracts) and in vivo (in protoplasts). Next, genome-wide H3K9/14ac profiles in Arabidopsis seedlings were generated by ChIP-sequencing and changes induced by GSNO, GSNO/cPTIO or trichostatin A (HDAC inhibitor) were quantified thereby identifying genes which display putative NO-regulated histone acetylation. Functional classification of these genes revealed that many of them are involved in the plant defense response and the abiotic stress response. Furthermore, salicylic acid (SA), which is the major plant defense hormone against biotrophic pathogens, inhibited HDAC activity and increased histone acetylation by inducing endogenous NO production. These data suggest, that NO affects histone acetylation by targeting and inhibiting HDAC complexes, resulting in the hyperacetylation of specific genes. This mechanism might operate in the plant stress response by facilitating stress-induced transcription of genes.