Background: Abrus precatorius is also called as Gunja in Ayurveda. It is a commonly grown plant belonging to the family of Fabaceae. It is characterized under the Upavisha (semi-poisonous drugs) and used widely in various Ayurvedic formulations with great beneficial significance. It is used in the treatment of various diseases such as alopecia, edema, helminthiasis, skin diseases, itching, and urinary disorders after being passed through specific purification procedures. Objectives: The present study aims to compare three different varieties of A. precatorius which includes the species of white, black, and red which are used to study DNA barcoding marker and phylogenetic analysis. Materials and Methods: Whole genomic isolated DNA from three varieties (white, black, and red) of A. precatorius leaves and subjected to analysis of the polymerase chain reaction of rbcL, maturase K, and internal transcribed spacer 4,5 using 0.8% agarose gel electrophoresis. Results: The DNA barcoding markers and next-generation sequencing can identify the intraspecies genetic variations among these closely related plant varieties of A. precatorius of white, black, and red. Conclusion: The intraspecies genetic variations among these three varieties of A. precatorius white, black, and red are closely related with A. precatorius isolate TMP 144 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit gene 99.81%.