Under the light microscope, eyespots appear as dark, orange-reddish spots or stigmata. They get their color from carotenoid pigments contained in bodies called pigment granules.  The photoreceptors are found in the plasma membrane overlaying the pigmented bodies.
The eyespot apparatus of Euglena comprises the paraflagellar body connecting the eyespot to the flagellum. In electron microscopy, the eyespot apparatus appears as a highly ordered lamellar structure formed by membranous rods in a helical arrangement.
In Chlamydomonas, the eyespot is part of the chloroplast and takes on the appearance of a membranous sandwich structure. It is assembled from chloroplast membranes (outer, inner, and thylakoid membranes) and carotenoid-filled granules overlaid by plasma membrane. The stacks of granules act as a quarter-wave plate, reflecting incoming photons back to the overlying photoreceptors, while shielding the photoreceptors from light coming from other directions.  It disassembles during cell division and reforms in the daughter cells in an asymmetric fashion in relation to the cytoskeleton.  This asymmetric positioning of the eyespot in the cell is essential for proper phototaxis.