The efficient micropropagation procedures among four Mentha species (M. longifolia, M. spicata, M. viridis, and M. piperita) were established. In addition, the shoots were produced in 3.0 mg/l BA. M. longifolia had the highest percentage of regeneration (70%), whereas M. piperita recorded that the lowest value (47%). The micropropagated plants and field plants were subjected to phytochemical analyses. The gas chromatography and spectrophotometer results indicated that the active ingredients were changed in the regenerated plants. Nevertheless, the results of molecular markers showed that the thirteen SRAP primer combinations had 80 scorable bands; of them, 58 were polymorphic (72%). Nine ISSR markers showed a total of 60 scorable bands; of them, 44 were polymorphic (73%). Twelve out of the 102 polymorphic SRAP and ISSR markers were found to be genotype unique specific markers.