Reversible histone acetylation and deacetylation at the N-terminus of histone tails play a crucial role in regulation of eukaryotic gene activity. Acetylation of core histones usually induces an "open" chromatin structure and is associated with gene activation, whereas deacetylation of histone is often correlated with "closed" chromatin and gene repression. Histone deacetylation is catalyzed by histone deacetylases (HDACs). A growing number of studies have demonstrated the importance of histone deacetylation/acetylation on genome stability, transcriptional regulation and development in plants. Furthermore, HDACs were shown to interact with various chromatin remolding factors and transcription factors involved in transcriptional repression in multiple developmental processes. In this review, we summarized recent findings on the transcriptional repression mediated by HDACs in plants.