The genetic diversity of wild thyme (Thymus capitatus) which growing  in southern parts of Al-Jabal Al-Akhdar region, Libya was studied by using cluster analysis of morphological traits (flower measurements). This study was aimed to establish the phylogenetic relationships based on floral parameters among accessions of thyme (T.capitatus). The five populations (accessions) of Libyan thyme were assigned into two clusters (clades) at the critical distance value of 22%. The 1stcluster  contained three populations that were included white-flowered, dotted white-flowered and violet-flowered accession, then the 1st cluster was divided into two sub-clusters by the critical distance value of 5%, the first sub-cluster contained two populations (white-flowered, dotted white-flowered accession). While, the second sub-cluster contained one population (violet-flowered accession). The 2nd cluster contained two populations which were purple-flowered and mosaic-flowered accessions. In conclusion, The flower measurements can be a preliminary tool to classify Libyan thyme (T.capitatus), and  floral parameters can be used in the classification of Libyan thyme accessions (populations).