Many economically important crops are infected with phytoplasmas, which are obligatory bacteria that do not contain a cell wall and cause great losses in crops around the world. Little information is known about the mechanisms of phytoplasma interaction with the host plants including sesame , especially on the quantity and quality of seeds' oil. Therefore,  to study the effect of phytoplasma on the anatomical structure of different plant organs, , especially the capsules that contain oil-producing seeds. Samples were collected from the healthy and infected plants, which showed symptoms of phyllody, and cross sections were made in the stem, leaf and capsule. Results indicated that the thickness of the stem as well as the leaf was increased, mainly due to the increase in proportions of the vascular bundles. In the capsule, on the other hand, the pericarp shrank, the false septum dissolved in the ovary, and leaves formed instead of seeds inside the capsule. The obtained results provide a better insight on the effect of phytoplasmaon the anatomical structure of the host plant, for exploring effective ways to control the disease.