Cananga odorata (Lam.) Hook.f. & Thomson, a member of the Annonaceae family, has become widespread from the Indo-Malayan region to northern Australia and Malaysia. This plant has economic value because it produces essential oils used in the perfume and food industries. No research existed yet related to DNA barcoding to see intraspecific variations in C. odorata. This study aimed to analyze the potential of chloroplast genes maturase K (matK)-trnK, ribulose 1,5-biphosphate carboxylase (rbcL), and trnL-F intergenic spacer as DNA barcodes on C. odorata from North Sumatra, Indonesia. The research sample obtained from five areas included Tanjung Balai, Langkat Regency (Tangkahan Conservation Forest), Medan, Tanjung Morawa (Deli Serdang Regency), and Sukarasa (Deli Serdang Regency). Phylogenetic analysis using the three markers showed that C. odorata was monophyletic grouped from a common ancestor. The results of the phylogenetic tree construction also showed that the three markers used were able to group each genus in the Annonaceae family and form separate branches from the outgroup (Magnolia, Sarcandra, and Litsea). The barcoding gap on the genetic distance could not be observed in this study, although phylogenetic results showed that the three markers were discriminatory enough to separate species. The results showed that the matK-trnK, rbcL, and trnL-F markers could be effectively used as DNA barcodes to identify C. odorata.