Abstract The orientation of the pigments in cells, thylakoids and isolated pigment-protein complexes of two chromophytic algae containing fucoxanthin as the principle carotenoid, has been investigated by linear dichroism spectroscopy. The Q y transition of both chlorophyll a (chl a) and chlorophyll c (chl c) is oriented at < 35° to the plane of the thylakoid membrane and to the long axis of the cells. The fucoxanthin transition, centred at 540 nm, is oriented in the same manner. In the isolated light-harvesting complexes, in compressed polyacrylamide gels, the linear dichroism specta suggest a different orientation of all pigments, i.e., < 55° to the direction of applied force or 35° to the long axis of the particle. It is demonstrated that this orientation is an artefact arising from decomposition of the light-harvesting complex during its preparation in the compressed polyacrylamide gel. The pigments of isolated PS I and PS II complexes retain the orientation they show in thylakoids and whole cells.