Pelargonium sidoides is indigenous to South Africa and abundant in the Eastern Cape Province. Several herbal products have been formulated using P.sidoides of which Umckaloabo® is probably the most popular and successfully marketed in Germany. The objective of this study was to discriminate between P.sidoides and P.reniforme by FT-IR spectroscopy. Absorbance spectra were collected for P.sidoides (n = 96) and its close taxonomic ally P.reniforme (n= 57) in the near infrared (NIR) and mid infrared (MIR) regions. The spectroscopic data was analysed using chemometric computations including principal component analysis and orthogonal projections to latent structures discriminant analysis. Phytochemical variation of 5.79% in the NIR dataset (R2X(cum) = 0.962; Q2(cum) = 0.918) and 9.22% variation in the MIR dataset (R2X(cum) = 0.497; Q2(cum) = 0.658) was responsible for the separation of the two species. Seven absorption areas were identified as putative biomarkers responsible for the differences between the two species. These results indicate that FT-NIR and FT-MIR spectroscopy can be used to discriminate between these two closely related species which occupy a sympatric distribution in South Africa.