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Chili pepper (<i>Capsicum</i><i> annuum</i>) is an important fruit and spice used globally, but its yield is seriously threatened by anthracnose. <i>Capsicum baccatum</i> is particularly valuable as it carries advantageous disease resistance genes. However, most of the genes remain to be identified. In this study, we identified the <i>C. baccatum</i>-specific gene <i>CbCN</i>, which encodes a truncated nucleotide-binding and leucine-rich repeat protein in the anthracnose resistant chili pepper variety PBC80. The transcription of <i>CbCN</i> was greater in PBC80 than it was in the susceptible variety An-S after <i>Colletotrichum acutatum</i> inoculation. In order to investigate the biological function of CbCN, we generated transgenic tobacco lines constitutively expressing <i>CbCN</i>. Notably, <i>CbCN</i>-overexpressing transgenic plants exhibited enhanced resistance to <i>C. acutatum</i> compared to wild-type plants. Moreover, the expression of pathogenesis-related (<i>PR</i>) genes was remarkably increased in a <i>CbCN</i>-overexpressing tobacco plants. In order to confirm these results in chili pepper, we silenced the <i>CbCN</i> gene using the virus-induced gene silencing system. The anthracnose resistance and expressions of <i>PR1</i>, <i>PR2</i>, and <i>NPR1</i> were significantly reduced in <i>CbCN</i>-silenced chili peppers after <i>C. acutatum</i> inoculations. These results indicate that CbCN enhances the innate immunity against anthracnose caused by <i>C. acutatum</i> by regulating defense response genes.