Many plant species show chemical polymorphisms regarding the composition of specialized metabolites belonging to certain chemical families. This led to the classification of chemotypes, that is, groups of plants that can be distinguished by their chemical profiles of metabolites within one chemical family. We present existing definitions and approaches for classifying chemotypes, and describe factors determining them. We argue that it should always be made explicit on which organ the chemotype specification is based, because chemical profiles can differ among organs. Moreover, the chemical family needs to be explicitly stated, as plants may be grouped differently when other metabolites are taken into account. We argue that gaining more knowledge on chemotypes is of high relevance for basic and applied science.