The distinct blue essential oil obtained from Eriocephalus sp. (Asteraceae) is known in commerce as Cape chamomile and has become an important ingredient in flavour and fragrance formulations. To date, it is commonly accepted that Cape chamomile oil is obtained from Eriocephalus punctulatus. Samples of E. tenuifolius DC (n = 35) and E. punctulatus DC (n = 17) were collected from different localities in South Africa and Lesotho. The hydrodistilled essential oil was analysed by gas chromatography coupled to mass selective detector and flame ionisation detector (GC-MS-FID). The GC-MS data was exported to MetAlignTM for spectral alignment and differentiation. The mid-infrared red (MIR) spectral data was processed using principal component analysis (PCA), partial least squares (PLS) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) algorithms. The oil from E. punctulatus showed a different profile from the commercial sample which mostly contained 1,8-cineole, piperitone, yomogi alcohol and pogostol. MetAlign successfully discriminated between the oil obtained from the two species and this data together with multivariate analysis showed that the commercial oil was similar to E. tenuifolius oil. Using the MIR data, a three component OPLS-DA model was constructed which convincingly discriminated between E. tenuifolius and E. punctulatus oil. The developed model further predicted the botanical origin of the commercial oils to be E. tenuifolius. The statistical performance of the model was excellent with an R2X (cum) = 0.897; R2Y (cum) = 0.991 and Q2Y (cum) = 0.987.