Salpingoeca cells are uninucleate (have one nucleus) and have one or more mitochondria, dispersed throughout the cell. The theca is visible as a thin vaselike structure surrounding the cell, often closely appressed to the cell surface. At the anterior end of the cell, a pair of basal bodies appears, only one of which is associated with an emergent flagellum. An electron-dense peripheral ring surrounds the flagellum-bearing basal body. Beneath the basal body complex, a single Golgi body occurs. Tentacles arise from various regions around the cell and extend apically to form the collar. Food particles are attached to the tentacles and transported to the cell body, where they are digested in food vacuoles

The mitochondrial cristae are flattened.

As in other choanoflagellates such as Monosiga, the cytoskeleton is based on a symmetrical system of radially arranged microtubules surrounding a single flagellar base.