Abstract: Background and Objective: Teucrium in Libya is represented by 11 species, five of which are endemic and among them problems at different taxonomic levels. Besides, Libya suffers from both human and environmental pressures and population fragmentation, which in turn lead to the loss of genetic diversity. There is an urgent need to assess this diversity therefor the aim of this study was to investigate the diversity among and within Teucrium as a prerequisite for conservation programming. Materials and Methods: The genetic diversity was assessed for 12 Teucrium taxa by RAPD and ISSR. Both the total and specific bands, polymorphism percentage, Shannon index (H) and Simpson index (D) were determined and the data was processed with cluster and principal component analyses. Results: Teucrium taxa were characterized with relatively low genetic diversity, particularly T. polium subsp. flavovirens. It was noted that the taxa of each section were not grouped together and the dendrogram resulted in a distinct sorting among the taxa at 0.545 similarity level. Both cluster and PCA analyses were clearly separated between T. capitatum and T. polium at the level of dissimilarity on par with other species. Conclusion: The study accepted T. capitatum and T. polium as two separate species and T. polium subsp. flavovirens as T. luteum subsp. flavovirens and for both Girian and Siert taxa, there was a doubt that they were assembled under T. polium which need to be confirmed by matching with other Teucrium species.