Peru has a great diversity of genetic resources, but at the same time, species are wasted due to ignorance or low economic performance. The situation reflected in the Huaura valley with the fruit trees of cansaboca (Bunchosia armeniaca), palillo (Campomanesia lineatifolia) and sour orange (Citrus aurantium), species with great importance in the traditional local gastronomy, but currently classified as endangered critically. To conserve these species, the objective was to establish DNA barcoding of three threatened species with economic potential in the Huaura Valley. DNA from the three species was extracted with the CTAB method, and universal DNA barcode primers belonging to chloroplasts were used for the PCR amplifications: matK, rbcL, and trnH-psbA. Samples were sequenced from the purified and quantified products. The sequences were analyzed, aligned, and grouped with the Bioedit, Codon Code Aligner, and MEGA programs. The DNA concentrations were: cansaboca (457 ng / μl), palillo (433 ng / μl) and sour orange (442 ng / μl). Amplification of the primers produced PCR products between 357 and 810 bp. The NCBI sequences that presented the highest percentage of identity with each species under study were subjected to phylogenetic analysis, which placed the species in different groups and revealed genetic differences with the studied samples. The essential tools were provided to implement DNA barcoding in three species of fruit trees in the Huaura valley.