Background: The genuineness of Ayurvedic herbs causally determines the effectiveness of Ayurvedic treatment protocols. Research and subsequent evidence-based medicinal practices fundamentally dependant on appropriate identification and standardization of specific herbs are used for health-care purposes. Definite deficits that prevail in this regard in the form of adulteration, substitution, and compromised quality standards are the reasons why many scientific communities and health-related organizations question Ayurvedic sciences. This study aims at raising the very timely subject matter of genuine drug collection based on a model of Pharmacognostical and high-performance thin-layer chromatography (HPTLC) profiling of an Indian medicinal herb "Manjishta"' (Rubia cordifolia L.), a profoundly marketed Ayurvedic drug. Objectives: To compare the six market samples of Manjishta (Pharmacognostical and with HPTLC profiling) with the genuine root and stolon. Materials and Methods: The market samples of Manjishta from 6 districts of Kerala were collected, and these samples were compared with the genuine root and stolon (morphology, histology, and with HPTLC profiles). Results: Morphological and anatomical evaluation of the market samples was similar with that of the original stolon of Rubia cordifolia. HPTLC profiling yielded entirely different peaks in specific samples when compared with that of the genuine stolon. Conclusion: The collected market samples of Manjishta from different districts of Kerala were almost similar to the stolon of Rubia cordifolia L. A clear standard operative procedure should be prepared for medicinal plant part collection with respect to source plant maturity for Manjishta or as a matter of fact any other herb and thus the HPTLC profiles should be redefined.