The paper aimed at studying the morphometric variation in eight natural populations of two rare Sideritis species occurring in Bulgaria. Thirteen measured traits and four ratios were used to reveal the degree and distribution of variation. Most traits exhibited moderate to high variation and the most differentiating one was the length of the acumen. Cluster analysis and Principal component analysis revealed that the two taxa, S. scardica and S. syriaca are well distinguished but the population Chervenata stena, classified as S. scardica differed significantly from the remaining ones of the same species. Results of the morphometric study indicate the necessity of further studies for revealing the taxonomic relationships among the taxa.