Merriam-Webster defines chemotaxonomy as the method of biological classification based on similarities and dissimilarity in the structure of certain compounds among the organisms being classified. Advocates argue that, as proteins are more closely controlled by genes and less subjected to natural selection than the anatomical features, they are more reliable indicators of genetic relationships. The compounds studied most are proteins, amino acids, nucleic acids, peptides etc.

Physiology is the study of working of organs in a living being. Since working of the organs involves chemicals of the body, these compounds are called biochemical evidences. The study of morphological change has shown that there are changes in the structure of animals which result in evolution. When changes take place in the structure of a living organism, they will naturally be accompanied by changes in the physiological or biochemical processes.

John Griffith Vaughan was one of the pioneers of chemotaxonomy.