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Different species/populations of Origanum and Thymus indigenous to Lebanon were analyzed by slab gel electrophoresis to compare protein patterns and isoenzymes phenotypes of esterase and peroxidase. Multiple electromorphs were obtained. The differences in the esterase profiles obtained by electrophoresis were consistent with the results of morphological identification of different groups of Origanum from different geographical areas. The esterase patterns successfully differentiate between different phenotypes/species of Origanum also between two different species of Thymus. The results demonstrated that isoenzymes phenotypes are useful to supplement the morphological characterisation of these species. The highest esterase activities and clearer banding profile were obtained during and after flowering period of plant development.