FD, a conserved bZIP transcription factor, is well known for its role in promoting flowering. Here, we uncover that a short coding sequence of the Chrysanthemum morifolium FD gene, CmFDa, represses flowering. Interestingly, we identified CmFDa as a novel epiallele stringently regulated by DNA methylation in chrysanthemum for the first time. Epigenetic editing of the CmFDa promoter using the CRISPR-dCas9-TET1cd for demethylation or dCas9-SunTag-NtDRM2cd for methylation can, respectively, repress or promote flowering. CmFDa epigenetically represses the floral transition by suppressing the expression of the floral activators CmSOC1 and CmAP1. We show that CmFDa recruits the Polycomb-repressive complex 2 (PRC2) to the CmSOC1 and CmAP1 promoters. These results reveal that CmFDa is an inhibitor of flowering by epigenetic repression of flowering integrator genes. This study provides a novel strategy for the epigenetic improvement of flowering time in plants.