Thymus is a species-rich and as well as a taxonomically complex genus. To address its diversity, taxonomic, biogeographical, and evolutionary uncertainties in the flora of Iran, detailed investigations are essential. During extensive botanical fieldwork and herbarium studies, three species Th. syriacus (West Iran), Th. coriifolius, and Th. jankae (Northwest Iran) were identified as new. These species are described in detail, with emphasis on their taxonomic, ecological, phenological, and biogeographical characteristics. By the current record of Thymus syriacus, distribution of Th. sect. Hyphodromii subsect. Thymprobsis is extended from Morocco to Iran highlighting a floristic connection between the Irano-Turanian (West Asia) and Mediterranean (North Africa) regions. Previously considered a Caucasian endemic, Th. coriifolius was found in the Arasbaran region of Iran, which biogeographically aligns with the Iranian highlands of the Caucasus. Similarly, Th. jankae, previously documented from the Balkans to Northeast Türkiye, is reported from the Caucasian highlands of Northwest Iran (Arasbaran). This finding reveals a significant spatial disjunction of approximately 500 km. The occurrence of both Th. coriifolius and Th. jankae in the Arasbaran Biosphere Reserve underscores the biogeographical homogeneity of the Caucasus ecoregion. Notably, the Caucasus highlands of Iran are now recognized as one of the richest habitats for Thymus. Finally, identification keys for these species are provided. To facilitate accurate identification, comprehensive descriptions of each species, along with a combination of diagnostic characteristics are essential.