In this study, the content of anthocyanins and the expression profile of regulatory (CaMYB113, CaMYB1, and CaMYB1-like) and structural (CaCHS, CaCHI, CaF3H, CaDFR, CaANS, CaUFGT1, and CaGSTF12) genes of the anthocyanin biosynthesis pathway were characterized in leaves, flower petals, and peel of unripe fruits of Capsicum frutescens L. pepper cultivars (Samotsvet, Rozhdestvenskii buket, and Evrika), which differ in the pattern of anthocyanin-mediated pigmentation of aboveground organs. A positive correlation of the CaCHS, CaF3H, CaDFR, CaANS, and CaCSTF12 transcript levels with the amount of anthocyanins in the leaves of these cultivars was found. It was shown that only CaMYB113 out of the three regulatory genes is expressed. The presence of a 5'-UTR in CaMYB113 mRNA was confirmed based on the example of ten cultivars of three pepper Capsicum species. The second variant of the CaMYB113 allele with the insertion of the LINE-1 retrotransposon in intron I was found in the genome of cv. Rozhdestvenskii buket and Samotsvet with purple coloring of the analyzed organs.