In order to investigate the effect of changing the reproductive system on the morphological and phytochemical traits of mint plant, three plant populations belonging to M. longifolia (Karaj,Hamedan, Esfahan) and three plant populations belonging to M. spicata (Lorestan,Ahvaz, Dehbala) were evaluated for producing open and self- pollinated populations. All the plants in each population were first divided into two parts; one part was bagged before anthesis and the other part was left to be freely open pollinated. After collecting the seeds derived from self and open-pollinated plants, two genotypes belonging to M. longifolia (Karaj- Hamedan) and two additional genotypes belonging to M. spicata (Lorestan- Ahvaz) were selected based on their performance in seed germination test. In the following, an experiment was conducted using a randomized complete block design (RCBD) with three replications at the Research Farm of Isfahan University of Technology to investigate the effects of self and open pollination on morphological and phytochemical traits in two species of Mentha . According to the results, plant reproduction through sexual reproduction compared to asexual reproduction created a high diversity in the studied traits in both species.In two populations of Karaj and Hamedan belonging to M.longifolia , seedling production caused a relative decrease in vegetative traits such as plant height, crown diameter, stem diameter, leaf length and leaf width. While the mean of phytochemical traits not only did not decrease but also in the population of Hamedan, flavonoid content increased due to self pollination. In contrast, in Lorestan and Ahvaz populations, open pollination and self-pollination with a positive effect on the majority of morphological and phytochemical traits caused a significant improvement in the mean of these traits, so that for the production of maximum biological yield and the most desirable amount of phenolic and flavonoid compounds, the production of seedlings derived from open and self pollination in this species, is recommended. According to GC-MS analysis, changes in the reproductive system led to a decrease in polegon composition and an increase in mentone composition. In this regard, open and self-pollination in the population of Hamedan led to a decrease in the piperitoneon compond and increase in pulegon, although the increase in piperitoneon content was more evident in the self pollinated population of Hamedan. In contrast, open and self pollination in the populations of Ahvaz and Lorestan led to a decrease in limonene and carvone compounds, which was much greater in self pollinated population of Ahvaz, which probably indicates that the essential oil production processes of this population are affected by inbreeding. In order to identify superior and weaker phenotypes, single plants obtained from open and self pollination were planted in a randomized completely block design with three replications and distance of 100 cm. The evaluation of morphological and agronomic traits during the two consecutive years showed a wide range of diversity due to changing in the reproductive system. Evaluation of phytochemical traits of selected plants led to the identification of some superior seedlings of open pollinated population (ko27, ho14, ao32 and lo47) which had the highest essential oil yield and desirable phenolic and flavonoid content. Therefore, it is advisable to plant these seedlings instead of the parent plants of these populations. Self-pollination caused different reactions in populations due to the possible effects of inbreeding dpression. But especially in plants of Lorestan, selfing (ls17 and ls59) was associated with a significant increase in phenolic and flavonoid content as well as antioxidant capacity. In the present study, antimicrobial propertiesof plants against Staphylococcus aureus and Escherichia coli showed the superiority of selected plants in Lorestan population (lo47-ls17-ls59). HPLC analysis also showed the presence of three important compounds including rutin, luteolin and rosmarinic acid in the phenolic extracts of three selected plants, which according to the antibacterial properties of the above compounds, was consistent with the results of the microbial properties test.The results of expression of two genes (limonene synthase and limonene 3 hydroxylase) showed an increase in the expression of limonene synthase gene due to changingig reproductive system in most of the seedlings belonging to both species. While the expression of limonene 3 hydroxylasegene was less altered due to the pollination. Key words: Mentha - -Self pollination- Open pollination- Inbreeding depression-Phenol-Flavonoid