Premise of the study:We report the complete sequence of the chloroplast genome of Capsicum frutescens (Solanaceae), a species of chili pepper.Methods and Results:Using an Illumina platform, we sequenced the chloroplast genome of C. frutescens. The total length of the genome is 156,817 bp, and the overall GC content is 37.7%. A pair of 25,792‐bp inverted repeats is separated by small (17,853 bp) and large (87,380 bp) single‐copy regions. The C. frutescens chloroplast genome encodes 132 unique genes, including 87 protein‐coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Of these, seven genes are duplicated in the inverted repeats and 12 genes contain one or two introns. Comparative analysis with the reference chloroplast genome revealed 125 simple sequence repeat motifs and 34 variants, mostly located in the noncoding regions.Conclusions:The complete chloroplast genome sequence of C. frutescens reported here is a valuable genetic resource for Capsicum species.