During RNA-directed DNA methylation (RdDM), the DDR complex,composed of DRD1, DMS3, and RDM1, is responsible for recruitingDNA polymerase V (Pol V) to silence transposable elements (TEs) inplants. However, how the DDR complex is regulated remainsunexplored. Here, we show that the anaphase-promoting complex/cyclosome (APC/C) regulates the assembly of the DDR complex bytargeting DMS3 for degradation. We found that a substantial set ofRdDM loci was commonly de-repressed inapc/candpolvmutants,and that the defects in RdDM activity resulted from up-regulatedDMS3 protein levels, which finally caused reduced Pol V recruitment.DMS3 was ubiquitinated by APC/C for degradation in a D box-dependent manner. Competitive binding assays and gel filtrationanalyses showed that a proper level of DMS3 is critical for the as-sembly of the DDR complex. Consistent with the importance of thelevel of DMS3, overaccumulationof DMS3 caused defective RdDMactivity, phenocopying theapc/canddms3mutants. Moreover,DMS3 is expressed in a cell cycle-dependent manner. Collectively,these findings provide direct evidence as to how the assembly ofthe DDR complex is regulated and uncover a safeguarding role ofAPC/C in the regulation of RdDM activity.