Flowering time is tightly controlled by several regulatory pathways including photoperiod, vernalization in which epigenetic processes are involved. In this work, we have found that the Arabidopsis histone deacetylase gene HDA9 is involved in flowering time control. Mutation of the gene led to an early flowering phenotype in short day grown plants while without effect in long days. Analysis of flowering time regulatory gene expression revealed that hda9 mutations highly induced the expression of AGL19, but had no effect on CO, SOC1 or FLC. Chromatin immunoprecipitation assays indicated that the mutations led to a clear increase of histone H3K9 and H3K27 acetylation on the AGL19 gene in short days. AGL19 promotes flowering in a way independent of the CO and FLC pathways and has been shown to be repressed by polycomb group repressive complex2 (PRC2) EMF2 but activated by vernalization. The induced levels of AGL19 expression and histone acetylation by the hda9 mutations were comparable to that of the gene under long day conditions, indicating that AGL19 is regulated also by day length and that HDA9 is involved in short day repression of AGL19 by promoting histone H3 deacetylation, which may be related to the PRC2 EMF2 complex.