Fine structure of vegetative cells, development and morphology of sporangia and general morphology of zoospores were studied for the first time in the genus Endophyton Gardner. Vegetative cells contained one parietal perforate chloroplast with 2–4 ulvophycean pyrenoids and transverse cell walls without plasmodesmata. Sporangial walls were formed by two distinct electron-dense and fuzzy layers which contained a contiguous electron-translucent, fibrillar material. Zoospores were naked, with an anterior dense aggregation of vesicles and a cup-shaped chloroplast with one eyespot. The flagellar apparatus showed 180° rotational symmetry and counterclockwise absolute orientation of its components. Microtubular roots had a cruciate pattern, in which d=2 and s=4 with 3/1 arrangement. Electron-dense bilobed terminal caps covered the proximal end of each basal body. These observations support the suggested close relationship of Endophyton to the allied genus Entocladia and other ulvalean algae, and reinforce the criteria for including the genus in the class Ulvophyceae, order Ulvales, family Ulvellaceae.