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Objective To explore a detailed pharmacognostic study of the rhizome of Hedychium spicatum Ham-ex-Smith (Zingiberaceae), a plant species which is commonly used in preparation of indigenous medicine. Methods The macroscopy, microscopy, quantitative analysis, extractive values in ethanol and water, phytochemical screening, TLC and HPTLC of aqueous and ethanolic extract and DNA fingerprint of the rhizome were investigated. Results Rhizome appeared to be 15–20 cm long, 20–25 mm in diameter, light-brown with 4–6 nodules. Transverse section of rhizome showed an outermost thick layer of suberised, dark brown cells in outer cork with 10 or more layers of irregular parenchymatous cells. Inner cork consisted of a few layered light brown rectangular radially arranged cells, followed by a wide zone of cortex having 30–40 cell layers. Rhizome powder was light brown in colour, bitter having camphorous odour, and fibrous texture. Alkaloids, carbohydrates, proteins, resins, saponins, steroid, tannin, starch and glycosides were present in both extracts while, flavonoids and triterpenoids were present only in ethanolic extract. TLC, HPTLC and DNA fingerprinting confirmed the chemical composition present in rhizome. Conclusions The pharmacognostic profile of Hedychium spicatum rhizome is helpful in sample identification, quality and purity standards.