Endoreduplication is often associated with cell growth and differentiation in plants and animals, but molecular mechanisms of plant endoreduplication have not been fully understood. Here, we describe that the Mediator complex subunit MED16 acts as a negative regulator of endoreduplication to influence cell growth in Arabidopsis. The med16 mutations cause larger and more cells, resulting in large organs. The large cells in med16 are associated with high DNA ploidy levels. MED16 associates with the promoters of the Anaphase Promoting Complex/Cyclosome (APC/C) activators CCS52A1 and CCS52A2, which are the important factors for endoreduplication and cell growth in Arabidopsis, and represses their expression. MED16 interacts physically with the transcription repressor DEL1 to repress expression of CCS52A2. Genetic analyses suggest that MED16 is partially dependent on CCS52A1/A2 to control endoreduplication and cell growth. Thus, our results reveal that the transcriptional repression of CCS52A1/A2 by MED16 regulates endoreduplication and cell growth in Arabidopsis.