Morinda reticulata Gamble and Morinda umbellata Linn. (Rubiaceae) are medicinally important climbers distributed as a mixed population in southern Western Ghats of India. A close morphological resemblance of these two species misleads the harvester in the identification of plant parts for preparation of herbal medicines. Though both species contain anthraquinone derivatives and share common medicinal properties for treating stomach disorders, each of these species has unique curative properties for treating selective diseases. Conventional methods are not reliable for identification of these species due to similarities in morphology. Thus, misidentification often leads to the deterioration of the quality of medicines. Thus, authentication utilizing conserved gene sequences in the chloroplast genome of these two Morinda spp. has been attempted for precise identification. Here we report the use of two barcoding genes (maturase kinase and ribulose 1,5-bisphosphate carboxylase large subunit) to distinguish M. reticulata and M. umbellata based on single nucleotide polymorphism. The present findings can be used for authenticating leaf samples of M. reticulata and M. umbellata.