Thymus herba-barona is endemic to Majorca, Corsica, and Sardinia. In order to gain insight into its evolutionary history, we examined the genetic diversity and phylogeography of the species using sequences of the trnT-trnL intergenic spacer from 106 individuals belonging to 15 populations. We detected high within-species genetic diversity and strong among-population differentiation, but no evidence for phylogeographic structure. A haplotype network supported the occurrence of three main clades, the ancestral one being geographically restricted to the Gennargentu massif in Sardinia, while the two derived ones were relatively widespread. Coalescent-based analyses indicated deep divergence times and limited ongoing gene flow between major clades. The inferred evolutionary history of the species involved an early range expansion followed by successive fragmentation episodes, probably related to progressive climatic aridification since the Pliocene (3.2 Ma). Our data suggest that long-distance dispersal events played a minor role in the evolutionary history of the species. The exact origin of the species remains unclear. The highly structured pattern of genetic variability detected suggests that random genetic drift played a major role in structuring genetic variation in this endemic plant. The cytogenetic evidence does not support the proposed recognition of three taxonomic entities within T. herba-barona based on morphological discontinuities associated with different ploidy levels.