The morphological characters of Southeast Asia’s indigenous Peperomia species are very similar, especially in their flower structures. The flowers are simple, hermaphrodite and lack a perianth. Therefore, many species are hard to distinguish using morphological characters alone. Here, we apply chemometric data for species identification and classification, gathered using multiwavelength detection combined with the colour scale High-Performance Thin-Layer Chromatography (HPTLC) fingerprinting procedure and chemical compounds determined by Gas Chromatography–Mass Spectrometry (GC-MS). Fourteen taxa were investigated using hexane, ethyl acetate and ethanol solvent extractions. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were used with the colour scale fingerprints to classify the Peperomia species. The PCA and HCA using the chromatogram profile from hexane divided the taxa into six groups compared to the profile from ethyl acetate and ethanol, which each detected seven groups. The chromatogram from the combined dataset of all three solvents can differentiate all the species. The GC-MS data detected a total of 40 compounds from the hexane extract, and these differed among Peperomia species. This approach based on HPTLC fingerprinting and GC-MS analysis can therefore be used as a tool for authentication and identification studies of Peperomia species.