Histone acetylation and complexes associated with this process are directly involved in chromatin regulation and gene expression. Among these, NuA4 complex is directly involved in acetylation of histone H4, H2A and H2A.Z. In yeast, the NuA4 complex contains the catalytic subunit, the histone acetyltransferase ESA1, and several associated components including YAF9. In this report we explored the biological role of YAF9a in Arabidopsis thaliana. Homozygous yaf9a-1 and yaf9a-3 mutants show early flowering phenotypes. Moreover, yaf9a-1 mutants displayed reduced expression of the flowering repressor FLC, whereas the expression of the flowering activators FT and SOC1 was induced in comparison to wild-type plants. Using chromatin immunoprecipitation assays with H4 tetra-acetylated antibodies we observed a positive correlation with gene expression profile of FLC and FT in yaf9a-1 mutants under long days. We therefore conclude that YAF9a in Arabidopsis is a negative regulator of flowering by controlling the H4 acetylation levels in the FLC and FT chromatin.