Plant metabolite profiling reveals the diversity of secondary or specialized metabolites in the plant kingdom withits hundreds of thousands of species. Specialized plant metabolites constitute a vast class of chemicals posingsignificant challenges in analytical chemistry. In order to be of maximum scientific relevance, reports dealingwith these compounds and their source species must be transparent, make use of standards and reference ma-terials, and be based on correctly and traceably identified plant material. Essential aspects in qualitative plantmetabolite profiling include: (i) critical review of previous literature and a reasoned sampling strategy; (ii)transparent plant sampling with wild material documented by vouchers in public herbaria and, optimally, seedbanks; (iii) if possible, inclusion of generally available reference plant material; (iv) transparent, documentedstate-of-the art chemical analysis, ideally including chemical reference standards; (v) testing for artefacts duringpreparative extraction and isolation, using gentle analytical methods; (vi) careful chemical data interpretation,avoiding over- and misinterpretation and taking into account phytochemical complexity when assigning iden-tification confidence levels, and (vii) taking all previous scientific knowledge into account in reporting thescientific data. From the current stage of the phytochemical literature, selected comments and suggestions aregiven. In the past, proposed revisions of botanical taxonomy were sometimes based on metabolite profiles, butthis approach (“chemosystematics” or “chemotaxonomy”) is outdated due to the advent of DNA sequence-basedphylogenies. In contrast, systematic comparisons of plant metabolite profiles in a known phylogenetic frameworkremain relevant. This approach, known as chemophenetics, allows characterizing species and clades based ontheir array of specialized metabolites, aids in deducing the evolution of biosynthetic pathways and coevolution,and can serve in identifying new sources of rare and economically interesting natural products.