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Abstract Overlapping geographical occurrence, history of traditional use, confusion in species identification, and morphological resemblances among various species are some considerations that necessitate the importance of qualitative analysis for efficient quality control and safer botanical products. This paper provides detailed morpho-anatomies of the leaves and stems of Tinospora cordifolia, Tinospora crispa, and Tinospora sinensis, and stems of Tinospora baenzigeri. Microscopy studies of the selected Tinospora species revealed key diagnostic features that can help distinguish the closely related species of Tinospora as well as to detect any adulteration or substitution in the raw materials. HPTLC profiles of the authenticated plant materials, as well as commercial products claiming to contain Tinospora, were compared to distinguish T. crispa from other closely related species and to establish an efficient method to assess the identity and quality of the products using qualified chemical markers. HPTLC chromatograms of both plant samples and dietary supplements were compared with six reference marker compounds. The analysis revealed that borapetoside B and C were useful to identify T. crispa while tinosineside A was found to be characteristic to authenticate the T. sinensis products.