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A chemotype (sometimes chemovar) is a chemically distinct entity in a plant or microorganism, with differences in the composition of the secondary metabolites. Minor genetic and epigenetic changes with little or no effect on morphology may produce large changes in the chemical phenotype.

A good example of a plant with many chemotypes is Thymus vulgaris. While largely indistinguishable in appearance, specimens of T. vulgaris may be assigned to one of six different chemotypes, depending on whether the primary component of the essential oil is thymol, carvacrol, linalool, geraniol, thujanol-4 or terpineol. Such chemotypes may be indicated as Thymus vulgaris ct. thymol (red thyme), or Thymus vulgaris ct. geraniol (sweet thyme), etc. Such an indication has no taxonomic standing, also see ecotype.