Abstract An investigation by GC/MS into the composition and variability of the essential oils contained in 63 individual plants taken from 21 populations of Thymus zygis L. in Southern Spain was carried out. Chemometric investigation of the infraspecific variability of the essential oils of these populations led to the differentiation of seven main chemotypes: thymol, carvacrol, linalool, α-terpinyl acetate, thymol/p-cymene/γ-terpinene, 1,8-cineole/myrcene/spathulenol and 1,8-cineole/α-terpineol. The phenolic compound thymol was the most common constituent in the majority of the samples studied. The concentration of its precursors, p-cymene and γ-terpinene was also noteworthy. There was no chemotaxonomic differentiation between the two subspecies (gracilis and sylvestris) for the Thymus zygis plants studied