Beginning in the 1990s, the growth of molecular phylogenetics led to the findings that existing concepts of Satureja and Micromeria were polyphyletic and led to more circumscribed monophyletic definitions of these genera. In 1995, Philip D. Cantino and Steven J. Wagstaff, carried out the first molecular phylogenetic tree that included this species, based on a restriction site analysis. They concluded that Calamintha and a number of New World Mentheae genera and species, including then-Satureja douglasii, formed a distinct clade separate from Satureja sensu stricto (represented by Satureja montana) and from Micromeria. In 1998, they recommended use of Clinopodium as a synonym for Calamintha and that the former was the older name that took priority, and that species of sect. Hesperothymus also be transferred to a new, broadly-defined genus Clinopodium, specifically listing Clinopodium douglasii (Benth.) Kuntze as the preferred name for this species. This concept of Clinopodium was endorsed in later synoptical works on the family Lamiaceae and the genus Micromeria published in the 2000s.
Beginning in the 1990s, the growth of molecular phylogenetics led to the findings that existing concepts of Satureja and Micromeria were polyphyletic and led to more circumscribed monophyletic definitions of these genera. In 1995, Philip D. Cantino and Steven J. Wagstaff, carried out the first molecular phylogenetic tree that included this species, based on a restriction site analysis. They concluded that Calamintha and a number of New World Mentheae genera and species, including then-Satureja douglasii, formed a distinct clade separate from Satureja sensu stricto (represented by Satureja montana) and from Micromeria. In 1998, they recommended use of Clinopodium as a synonym for Calamintha and that the former was the older name that took priority, and that species of sect. Hesperothymus also be transferred to a new, broadly-defined genus Clinopodium, specifically listing Clinopodium douglasii (Benth.) Kuntze as the preferred name for this species. This concept of Clinopodium was endorsed in later synoptical works on the family Lamiaceae and the genus Micromeria published in the 2000s