This research was aimed to investigate the effects of biological fertilizers on seedling survival rate of Thymus pubescens Bioss. The study was conducted in the research field of Alborz Research Station in 2011 using a factorial arrangement in a randomized complete blocks design with three replications. Treatments included seed inoculation (Glomus intraradices, G. mosseae and without inoculation) and seedling inoculation (Glomus intraradices, G. mosseae and without inoculation). Analysis of variance indicated that seed inoculation significantly affected canopy circle, number of tillers, number of lateral branches, plant height, seedling survival rate, seed colonization rate and shoot yield at p≤0.01 and flowering percentage at p≤0.05. According to the mean comparisons, the highest canopy circle, number of tillers, number of lateral branches, plant height, flowering percentage, seedling survival rate, root colonization rate and shoot yield were obtained for seed inoculation with G. intraradices. In addition, the highest number of tillers, number of lateral branches, plant height, root length, number of lateral roots, root colonization rate, essential oil percentage and shoot yield were obtained for seedling inoculation with G. intraradices. Consequently, in terms of essential oil percentage and shoot yield, better results were recorded for seed inoculation as compared to seedling inoculation.