Harpagophytum procumbens (Burch.) DC. ex Meisn. subsp. procumbens (Pedaliaceae) is an important African medicinal plant growing in the Kalahari region of southern Africa. This species, together with its close taxonomic ally H. zeyheri are collectively referred to as Devil’s Claw and are used interchangeably for the treatment of inflammation-related disorders. Although the two taxa are botanically and chemically similar, H. zeyheri contains lower levels of harpagoside and these two species have not been proven to exhibit equipotent pharmacological activity. Due to these taxonomic similarities, effective quality control methods are required to distinguish between the two species. Differentiation between the two species was achieved using single point mid-infrared spectroscopy in combination with chemometric data analysis. The orthogonal projections to latent structures discriminant analysis (OPLS-DA) model had good predictive ability, as illustrated by the model statistics: R2X (cum predictive + orthogonal) = 0.86 and Q2 (cum) = 0.63. Short wave infrared (SWIR) hyperspectral imaging could distinguish between the two species with acceptable model statistics; R2X and R2Y of 0.99 and 0.78, respectively. This study demonstrated that both MIR single point spectroscopy and SWIR hyperspectral imaging coupled with chemometric modeling is a reliable and rapid method to determine the authenticity of Harpagophytum spp.