Echinacea species are popularly included in various formulations to treat upper respiratory tract infections. These products are of commercial importance, with a collective sales figure of $132 million in 2009. Due to their close taxonomic alliance it is difficult to distinguish between the three Echinacea species and incidences of incorrectly labeled commercial products have been reported. The potential of hyperspectral imaging as a rapid quality control method for raw material and products containing Echinacea species was investigated. Hyperspectral images of root and leaf material of authentic Echinacea species (E. angustifolia, E. pallida and E. purpurea) were acquired using a sisuChema shortwave infrared (SWIR) hyperspectral pushbroom imaging system with a spectral range of 920-2514 nm. Principal component analysis (PCA) plots showed a clear distinction between the root and leaf samples of the three Echinacea species and further differentiated the roots of different species. A classification model with a high coefficient of determination was constructed to predict the identity of the species included in commercial products. The majority of products (12 out of 20) were convincingly predicted as containing E. purpurea, E. angustifolia or both. The use of ultra performance liquid chromatography-mass spectrometry (UPLC-MS) in the differentiation of the species presented a challenge due to chemical similarities between the solvent extracts. The results show that hyperspectral imaging is an objective and non-destructive quality control method for authenticating raw material.