Plants have been used as medicines for millennia and are major contributors to developed western pharmacopoeia. The Erythroxylum and Nectaropetalum genera belong to the Erythroxylaceae (coca) family, with select species capable of producing highly valued ‘blockbuster’ medicinal compounds including, amongst others atropine, cocaine, scopolamine, and tigloidine. Erythroxylum delagoense, E. emarginatum, E. pictum, N. capense and N. zuluense are indigenous to the south-east tropical regions of Africa. The morphological similarity between these taxa make identification to species-level troublesome and often unreliable, indicating a need for alternative identification methods. This study aimed to compare gas chromatography-mass spectrometry (GC-MS)- and nuclear magnetic resonance (NMR)-based metabolomics analyses with DNA barcoding to evaluate the identifying characteristics of these coca species. The results emphasise the importance of integrating chemotaxonomy and DNA barcoding techniques in plant identification. In this sample of the Erythroxylaceae, the differentiating identification accuracy was shown to increase from morphology to DNA barcoding to chemotaxonomy. This study further highlights the strengths and weaknesses of various plant identification strategies, as well as providing a developing model for more accurate and reliable species-level identification of plants. The findings from this case study could aid in the identification and classification of other closely related taxa.