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Introduction The genus Stachys L., belonging to the family Lamiaceae, is one of the largest genera with remarkable medicinal properties. Plants of this genus produce a broad range of secondary metabolites. Objectives Due to the incomplete comprehensive assessment of chemical profiles in Stachys species, we conducted an untargeted metabolomics study and identified potential biomarkers in the six sections of Stachys with chemotaxonomic importance. Material and Methods Dried leaves of 17 taxa were utilized for analysis of all the constituents using HPLC‐MQ‐API‐MS. The obtained data were processed and analyzed using multivariate statistical methods, including heatmaps, PLS‐DA score plots, functional analysis of metabolic pathways, metabolite set enrichment analysis, and biomarker and network analysis. Results Among the 129 metabolites, 111 flavonoids and 18 non‐flavonoids were recognized. The most represented flavonoids, including 41 flavones and 20 flavonols, displayed remarkable abundance. In non‐flavonoid compounds, a total of six coumarins and six phenolic acids were present at high levels. In terms of approved markers in six sections, 76 chemical compounds, mainly flavonoids, coumarins, quinic acids, and cinnamic acids, were identified as potential biomarkers or chemotaxonomic indicators. Accordingly, the taxonomic complexities of some Stachys species in sections Fragilicaulis, Aucheriana, and Setifolia were properly resolved. Conclusion An HPLC‐MS/MS‐based metabolomics approach integrated with multivariate statistical methods was employed to identify (1) valuable markers and analyze metabolic diversity and (2) predict the pharmaceutical properties of Stachys species. The obtained chemical profiles provide a new perspective for investigation of the Stachys genus.

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