Pomegranate fruit rot leads to lose of significant quantity of fruit worldwide. In present study, the antifungal effects of thymol on the morphology of Aspergillus niger and Penicillium commune as the main fungi causing pomegranate fruit rot investigated in in vitro conditions. Examination of cell morphology using scanning electron microscope (SEM) in Aspergillus niger colony showed that cell deformation was observed due to destruction of the cell membrane and loss of cell wall strength at concentration of 250 µg mL^-1 (FC50) after 168 h. Produced hyphae had irregular branching and no spore production was observed. Evaluation of Penicillium commune colony cell morphology using SEM showed that thymol at concentration of 250 µg mL^-1 (FC50) caused superficial wrinkles, bifurcation of hyphal apex and no spore production was observed.