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Chakhao Poireiton, Chakhao Sempak and Chakhao Amubi are the three most popular traditional non-Basmati-type black scented rice of the state of Manipur in India. These varieties have long statured (135-145 cm height) plants which have high anthocyanin pigment on sheaths, leaf blades, nodes and internodes. They are characterized by late heading (115-120 days) and late maturity duration (145-150 days). The lemma and palea of grains are of purple colour with strong fragrance. The agro-morphological characterization of Chakhao Poireiton, Chakhao Sempak and Chakhao Amubi was done at College of Agriculture, Central Agricultural University, Imphal, India during the wet (Kharif) seasons of 2017 and 2018 following the DUS test guidelines for the Protection of Plant Varieties and Farmers' Rights Authority (PPV & FRA). DNA extractions were done using SDS method and a CAPS marker for the OSB1 gene was used to discriminate rice seeds governing white and black colour. We validated the usefulness of this marker in three varieties of black scented rice and in a white local landrace as well as their crosses with the white local landrace.