We present a study on the taxonomy of eleven Thymus species, belonging to two sections and occurring naturally in Bulgaria. Four DNA barcoding markers—matK, rbcL, trnH-psbA and ITS—were applied to discriminate the species and to reveal their phylogenetic relationships. The results showed that rbcL has the lowest discriminating power regarding the studied species, while the other markers yielded results fitting better to the existing taxonomic schemes based on morphological traits. However, even in the case of better performing markers, the results were not straightforward—morphologically distinct species belonging to different sections were grouped together, and closely related species appeared genetically distinct. The results are typical for taxonomically complex groups, such as the genus Thymus, characterized in Bulgaria with great diversity, high percentage of endemism and still requiring a full and comprehensive taxonomic study. The results are discussed in the light of unresolved taxonomic problems and application of DNA barcoding methods.