Chemotaxonomy is a part of the taxonomy in the organism (mainly plant ) are classified in their biochemical composition due to the differences and similarities. Here it is taken into account that have shared here and especially the secondary metabolism during the evolution process metabolic processes and have different metabolic pathways, due developed in organisms by specific enzymes. The sister field of chemotaxonomy, the chemosystematics, explored on the basis of biochemical characteristics of the phylogenetic development.

Because some natural substances occur solely or principally with certain types, genders, families, or orders, this may be in addition to the morphology provide a basis for taxonomic classifications. Examples are the occurrence of Floridzine in apples, tariric at the Picramniaceae, colchicine in the lily family, lycorine in the family of Narcissus, Primula primin and betacyanin ( the nitrogen-containing dye of beetroot ) in the order Caryophyllales.

Due to the development of ever better methods of analysis are compounds that have been previously known only from certain plants, now also detected in lower concentrations in other plants. An example nicotine in a rather high concentration ( 4%) is present in plants of the genus Nicotiana tabacum is known, inter alia, by the usual tobacco plant Nicotiana. Nicotine appears in the plant kingdom of course also occur in other plants, but in much lower concentrations than in Nicotiana. Thus, this was not previously detected.

To a certain degree the chemotaxonomy is now experiencing a revival, as the research on chloroplast DNA gets a lot of attention. It happens that a group of plants that is now recognized on the basis of DNA values ​​, certain substances have in common; Substances, one of which was previously assumed that they are appeared several times in the plant kingdom, but now seem just very specific to occur only in some plant groups.

An important work in the chemotaxonomy is the thirteen part series chemotaxonomy of plants by Robert Hegnauer. In it, he describes the incidence per family, the operation and the biosynthesis of secondary plant substances. Other, more concise works are Chemical Plant Taxonomy by Tony Swain and systematics of the plant kingdom: With special consideration of chemical characteristics and herbal drugs by Dietrich Frohne and Uwe Jensen. Biochemical Systematics and Ecology is directed to Chemotaxonomy journal.