Abstract Aerenchyma is a characteristic tissue of aquatic plants, characterized by the presence of air lacunae commonly septated by diaphragms. These are formed by one or more layers of stellate cells, which allow for the passage of gases. Most species of Eleocharis grow in wet or flooded soils and have aerenchyma in their aerial stems. However, extensive studies on this structure, which could contribute to ecological and phylogenetic studies of the group, are lacking. This work describes the structure of the diaphragm in the stem of Eleocharis species and investigates the evolution of this characteristic in the genus. Fifty-three species were analyzed under light and scanning electron microscopy. We analyzed the evolution of the characteristics by reconstructing their ancestral states based on the previously published original phylogeny. The diaphragms in Eleocharis vary mainly in the number of layers, cell shape, and cell wall thickness. The typical diaphragm of the genus is composed of three to four layers of stellate cells, with microprojections and secretory cells. The diaphragm of the group’s ancestor had practically the same characteristics as the genus’s typical diaphragm.