Histone acetyltransferases, which are able to acetylate histone and non-histone proteins, play important roles in gene regulation. Many histone acetyltransferases are related to yeast Gcn5, a component of two transcription regulatory complexes SAGA and ADA. In this work, by characterizing a mutation in the Arabidopsis GCN5 gene (AtGCN5) we studied the regulatory function of this gene in controlling floral meristem activity. We show that in addition to pleiotropic effects on plant development, this mutation also leads to the production of terminal flowers. The flowers show homeotic transformations of petals into stamens and sepals into filamentous structures and produce ectopic carpels. The phenotypes correlate to an expansion of the expression domains within floral meristems of the key regulatory genes WUSCHEL (WUS) and AGAMOUS (AG). These results suggest that AtGCN5 is required to regulate the floral meristem activity through the WUS/AG pathway. This study brings new elements on the elucidation of specific developmental pathways regulated by AtGCN5 and on the control mechanism of meristem regulatory gene expression.