Calamus nambariensis Becc. is a high quality of rattan, threatened to the Northeastern region of India. The species was first described by O. Beccari based on a fragmentary specimen collected by G. Mann from Nambor Wildlife Sanctuary of Assam, India. In this study, an extensive survey was carried out to locate the occurrence of C. nambariensis in the Northeastern part of India and to determine their diversity and discrimination through morphological and molecular markers. Specimens collected from six localities; Nambor Wildlife Sanctuary (WLS), Hoollongapar Gibbon Sanctuary, Dehing Patkai WLS of Assam and Kimin, Khonsa and Namdapha National Park of Arunachal Pradesh showed considerable morphological variations among themselves. These differences are accommodated by assigning the status of subspecies as Calamus nambariensis subsp. nambariensis and Calamus nambariensis subsp. arunachalensis, and varieties such as Calamus nambariensis subsp. nambariensis var. nambariensis and Calamus nambariensis subsp. nambariensis var. hoollongapariensis. The taxonomic delimitation is also endorsed by matK, trnL-CD, and trnL-EF sequence analysis which strengthened our findings. The variations observed among the C. nambariensis occurring in northeastern India based on morphological and genetic diversity might be due to their adaptation in different biogeoclimatic conditions over the time.