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Pepper is renowned worldwide for its distinctive spicy flavor. While the gene expression characteristics of the capsaicinoid biosynthesis pathway have been extensively studied, there are already a few reports regarding transcriptional regulation in capsaicin biosynthesis. In this study, 73 <i>WRKYs</i> were identified in the genome of <i>Capsicum chinense</i>, and their physicochemical traits, DNA, and protein sequence characteristics were found to be complex. Combining RNA-seq and qRT-PCR data, the <i>WRKY</i> transcription factor <i>CA06g13580</i>, which was associated with the accumulation tendency of capsaicinoid, was screened and named <i>CcWRKY25</i>. <i>CcWRKY25</i> was highly expressed in the placenta of spicy peppers. The heterologous expression of <i>CcWRKY25</i> in <i>Arabidopsis</i> promoted the expression of genes <i>PAL</i>, <i>4CL1</i>, <i>4CL2</i>, <i>4CL3</i>, <i>CCR</i>, and <i>CCoAOMT</i> and led to the accumulation of lignin and flavonoids. Furthermore, the expression of the capsaicinoid biosynthesis pathway genes (CBGs) <i>pAMT</i>, <i>AT3</i>, and <i>KAS</i> was significantly reduced in <i>CcWRKY25</i>-silenced pepper plants, resulting in a decrease in the amount of capsaicin. However, there was no noticeable difference in lignin accumulation. The findings suggested that <i>CcWRKY25</i> could be involved in regulating capsaicinoid synthesis by promoting the expression of genes upstream of the phenylpropanoid pathway and inhibiting CBGs’ expression. Moreover, the results highlighted the role of <i>CcWRKY25</i> in controlling the pungency of pepper and suggested that the competitive relationship between lignin and capsaicin could also regulate the spiciness of the pepper.