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Anthocyanins are widespread water-soluble pigments in the plant kingdom. Anthocyanin accumulation is activated by the MYB-bHLH-WD40 (MBW) protein complex. In <i>Arabidopsis</i>, the R2R3-MYB transcription factor PAP1 activates anthocyanin biosynthesis. While prior research primarily focused on seedlings, seeds received limited attention. This study explores PAP1’s genome-wide target genes in anthocyanin biosynthesis in seeds. Our findings confirm that <i>PAP1</i> is a positive regulator of anthocyanin biosynthesis in <i>Arabidopsis</i> seeds. PAP1 significantly increased anthocyanin content in developing and mature seeds in <i>Arabidopsis</i>. Transcriptome analysis at 12 days after pollination reveals the upregulation of numerous genes involved in anthocyanin accumulation in <i>35S:PAP1</i> developing seeds. Chromatin immunoprecipitation and dual luciferase reporter assays demonstrate PAP1’s direct promotion of ten key genes and indirect upregulation of <i>TT8</i>, <i>TTG1,</i> and eight key genes during seed maturation, thus enhancing seed anthocyanin accumulation. These findings enhance our understanding of PAP1’s novel role in regulating anthocyanin accumulation in <i>Arabidopsis</i> seeds.