The mitochondrial genome data of the Capsicum annuum cv. Dempsey (Solanaceae)

<i>Capsicum annuum</i> L. (1753), commonly known as pepper, holds significant economic value as one of the globally cultivated horticultural crops. This study presents the mitochondrial genome of the sweet pepper <i>C. annuum</i> cv. Dempsey, assembled using Illumina NovaSeq data. The circular mitogenome is 577,453 base pairs (bp) in length and includes 36 protein-coding genes, three ribosomal RNA genes, and 43 transfer RNA genes. Phylogenetic analysis reveals that <i>C. annuum</i> is not monophyletic, with <i>C. annuum</i> cv. Dempsey identified as a sister to the hot pepper <i>C. annuum</i> cv. Jeju. This study provides as a valuable resource for comparative analyses of pepper mitogenomes, enhancing our understanding of the evolution and adaptive mechanisms of pepper species.