In the current work we evaluated the anatomical changes induced by T. harzianum and T. asperellum in two soybean cultivars, BRSGO Caiaponia and NA 5909 RG. Soybean production represents a growing market worldwide, and new methods aimed at increasing its productivity and yield are constantly being sought. Fungi of the genus Trichoderma have been widely used in agriculture as a promising alternative for the promotion of plant growth and for biological control of various pathogens. It is known that Trichoderma spp. colonize plant roots, but the anatomical changes that this fungus can cause are still less studied. Experiment was conducted in a greenhouse to collect leaves and soybean roots to perform analysis of growth parameters, enzymatic activity of defense-related enzymes and anatomical changes. It was observed that inoculation of Trichoderma spp. caused anatomical alterations, among them, increase in stomatal index at the abaxial leaf surface, thickness of the root cortex, thickness of adaxial epidermis, mean diameter of the vascular cylinder, thickness of the mesophyll, and thickness of the spongy parenchyma of the soybean plants. These results indicate that the alterations in these factors may be related to the process of plant resistance to pathogens, and better performance against adverse conditions. This study demonstrates that the anatomical study of plants is an important tool to show the effects that are induced by biological control agents.