IntroductionBhutanese Sowa Rigpa Medicine (BSM) uses two species of Aconitum in 25 important multi-ingredient formulations. The formulations are used for treating chronic disoders, parasitic and microbial infections, inflammatory diseases, bilious fever, or high fever related to bile disorders, including colds and flu. Some Aconitum species are toxic, and there is a need for stringent quality control measures. Materials and methodsAconitum orochryseum Stapf and Aconitum laciniatum (Bruehl) Stapf, were collected from Lingzhi, which is geographically located under Thimphu district, Bhutan, between the altitudes of 4000–4900 meters above sea level (masl), between July and September. Their comparative pharmacognostic properties were evaluated by: 1) using physicochemical parameters, such as foreign matter and moisture contents, total ash, acid-insoluble ash and alcohol-soluble extracts values and loss on drying of individual crude drugs; 2) developing a comparative High-Performance Thin Layer Chromatography (HPTLC) fingerprint, at Menjong Sorig Pharmaceuticals Corporation Limited (MSCPL), - Bhutan and 3) conducting a literature review to identify the nature and toxicity of alkaloids present in two Aconitum species. ResultsTwo Aconitum species possess distinct macros- and micros-copic characteristic features (including colour, taste, smell, appearance, and shape). The physicochemical analysis and the HPTLC fingerprinting of their methanol extracts yielded adequate data to differentiate and validate these two species’ identities, before adding them to 25 essential traditional medicine drugs (ETMDs) or polyherbal formulations in BSM. A literature review revealed that the two Aconitum species contained two distinct types of alkaloids. ConclusionsTwo Aconitum species could be differentiated based on their botanical features, macros- and micros-copic characteristics, physicochemical values and HPTLC fingerprint profiles. These pharmacognostic properties can be used as quality control parameters to confirm the two species' identity, thereby ensuring the quality and safety of BSM.