Pomegranate fruit rot by the fungi Penicillium spp., Aspergillus spp., Botrytis cinerea, Rhizopus spp., Nematospora spp. and Coniella spp. In present study, the antifungal effects of thymol on the growth of Aspergillus niger and Penicillium commune isolated from pomegranate fruits investigated in in vitro conditions. The experiment was performed as a factorial based on completely randomized design (CRD) with three replicates. The minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) of thymol for both fungi were 250 and 500 µg mL^-1, respectively. The lowest diameter of Penicillium commune colony (6.66 mm) was found at concentration of 250 µg mL^-1 after 168 h, however it was not significantly (P≤ 0.01) different with the diameter of Aspergillus niger colony at the same time. Thymol at the concentration of 500 µg mL^-1 had a similar effect as a fungicidal agent compared with thiabendazole (1500 µg mL^-1).