Insightful knowledge of plant secondary metabolites remains valuable in plant classifications, particularly for the establishment of the evolutionary relationship between species and authentication of medicinal plants. This PhD project aims to improve chemotaxonomy methods for complementing taxonomy classifications and quality control of herbal medicines. This work relies on high-resolution mass spectrometry metabolomics applied to the herbarium specimens of Gentianaceae family and field collections of Ficus deltoidea varieties. For this, rapid fingerprints of plant extracts and a molecular-network based annotation strategy for deep metabolome profiling were developed. This thesis illustrates the value of chemotaxonomy in the differentiation of closely related plant species and opens the possibility of using a small portion of herbarium collections for drug discovery. Finally, the in-depth chemical knowledge for F. deltoidea obtained in this thesis is now available as a foundation for future research in rationalizing its traditional therapeutic use.