Arnica flower (Arnica montana L.) is a valuable ingredient in many herbal and pharmaceutical products with anti-inflammatory properties. However, the pharmacopoeial herbal substance is often replaced by flower heads from other species, most often Heterotheca inuloides Cass. According to the European Pharmacopoeia one of the ways to distinguish drugs containing these two species is by TLC analysis of the rutin content in an aqueous ethanol extract. The present work proposes a method of distinguishing the two species based on exudate flavonoid profile, detected by HPTLC. Exudate flavonoid profiles of both species are distinguishable visually under UV light based on the different colouration of the main components. Methylated derivatives mainly of flavones were identified as the main component in the exudate of A. montana, whereas methylated flavonol derivatives were detected in the exudate of H. inuloides. The main components in H. inuloides are flavonoid aglycones coloured yellow (quercetin-3',3,7-trimethyl ether, quercetin-3,3',4',7-tetramethyl ether) or orange (quercetin, quercetin-3,7-dimethyl ether) under UV light. On the other hand, the main components found in A. montana (scutellarein-6-methyl ether, scutellarein-6,4'-dimethyl ether) are predominantly brown coloured. The proposed method is suitable for rapid identification of the Arnica flower containing drugs based on the profile of exudate flavonoid aglycones by the HPTLC technique.