Description of the two new sections and one subsection (sect. Oreokermatoria, sect. Brachyodontia, subsect. Inkermenia) of the genus Clinopodium L. is provided in the article. The new combinations Clinopodium sect. Pseudomelissa, C. albanicum, C. barbatum, C. brachycalyx, C. giresunicum, and a replacement name C. hispanicum are validated. Clinopodium barbatum, C. dalmaticum, C. frivaldszkyanum, C. molle, C. nummulariifolium, and C. serpyllifolium are lectotypified.