Thyme ( Thymus. ) is one of the most important genera of the mint family and is one of the oldest medicinal plants and spices. Inbreeding refers to the intercrossing of individuals whose kinship is much greater than that of individuals who accidentally intercross in a population. The most inbreeding state is the crossing of each person with itself through self-pollination. This study was conducted to estimate the effect of inbreeding on morphological traits and essential oil and phenol content of 11 self-pollinated populations in comparison with their open-pollinated populations in a randomized complete block design with three replications in Isfahan University of Technology Research Farm. Data analysis was performed for 17 morphological traits and essential oil and phenol content. The results of analysis of variance showed high variability between the studied populations for the traits that it indicates high variability in the studied germplasm. Within the open-pollinating populations, high diversity was observed for most traits. These results were also present within self-pollinating populations. Also, among the open-pollinated and self-pollinated populations, most of the studied traits became significant. The population of T. pubescence had the highest essential oil content due to self-fertilization and among all populations (self-pollinated and open-pollinated), the population of T. trautvetteri had the highest content of essential oil and the population of T. pubescence had the highest phenol content and the population of T. vulgaris had the highest wet and dry weight. Populations of T. daenensis-2 and T. fedtschenkoi-2 had a positive response to inbreeding and showed an increase in phenol content. The correlation was different between traits within open-pollinated and self-pollinated populatio For example, plant height with the number of inflorescences per plant and canopy diameter (in both open-pollinated and self-pollinated populations), number of flowers per inflorescence, inflorescence diameter, number and diameter of sub-stem and leaf length (in self-pollinated populations) had a positive relationship. By PC analysis, 5 PC were extracted in open-pollinated populations and 6 PC in self-pollinated populations, which together accounted for 87.68% and 93.81% of the changes, respectively. Based on cluster analysis, open-pollinated populations were divided into three groups and self-pollinated ones into three groups, but with different groupings. Gas chromatography identified 42 compounds in the essential oils of the populations, of which seven compounds of thymol, carvacrol, p-Cymene, ?-Terpinene, linalool, Terpinen-4ol, and ?-Terpineol were identified as major constituents in all populations. Also in self-pollinated populations Carvacrol methyl ether were among the main constituents; which had different correlations in populations. The principal component analysis of compounds with 6 main components explained 97.21% of the changes. Cluster analysis also Keywords : Thymus, self-pollinatin, open-pollinatain, inbreeding.