Here we report for the first time the ultrastructure of Halimeda discoidea, H. incrassata, H. opuntia, H. simulans and H. tuna, collected on the northeastern coast of Brazil. The genus is heteroplastidic, showing chloroplasts and amyloplasts in different stages of development. Large chloroplasts are more abundant in the cortical utricles, close to the outer cell walls, whereas small chloroplasts, amyloplasts, nuclei and mitochondria are more abundant in the medullary siphons. Chloroplasts are similar to those of terrestrial plants, with a system of thylakoids parallel to the chloroplast’s long axis and a large variation in the number of thylakoids per granum. A characteristic system of concentric lamellae is formed in one pole of the plastids. Chloroplast aging is characterized by an increase in number and size of the plastoglobules. In addition to the usual organelles, the cytoplasm has an unusual set of spherical bodies of different texture and electron-densities. Another kind of spherical bodies, with a fibrillar structure, is found inside the vacuoles. The function and composition of these bodies have not yet been ascertained.