Saussurea costus (Falc.) Lipchitz syn S. lappa C. B. Clarke (commonly known as 'Kuth') belonging to the family Asteraceae is a well known medicinal plant which finds wide usage in different indigenous systems of medicine of India, China, Korea & Tibet. In different folk medicines the roots of S. costus are used to treat various disorders like ulcer, stomachache, malaria, leprosy, dysentery and toothache. However due to over exploitation, it has become endangered and has become the concern of different governmental bodies in India. The increasing demand of this endangered Himalayan species has resulted in a situation where it is often substituted, knowingly or unknowingly, by other morphologically similar species. Arctium lappa, belonging to the same family, is one such plant that has often been found to be present in the market samples of 'Kuth'. The present study was thus carried out and morphoanatomical characters, physicochemical as well as chemical parameters were developed for proper identification of roots of S. costus and its differenciation from A. lappa as well as authentication of the commercial market samples. The detailed morphoanatomical studies revealed that roots of S. costus can be distinguished from A. lappa on the basis of some important microscopial characters eg. the schizogenous resin ducts observed in roots of S. costus, were absent in A. lappa.. Besides, the HPTLC fingerprint profile showed a distinct band at Rf. 0.72 in S. costus, which was totally absent in A. lappa and a band at $R_f$ 0.64 in A. lappa which was absent in S. costus Chlorogenic acid, used as a chemical marker for HPTLC analysis, was estimated to be 0.077% in S. costus as compared to 0.107% in A. lappa. Thus these detailed pharmacognostical parameters can be successfully used to distinguish between roots of S. costus and A. lappa.