Two species of fruticose lichens from different habitats and of distinct color, Usnea antarctica and Stereocaulon vesuvianum, were compared using chlorophyll fluorescence imaging in order to study the distribution of primary photosynthetic processes within the thalli. The thallus of U. antarctica is yellow with black tips: in this species chlorophyll containing cells were mostly located in the middle region of the thallus and the highest PS II efficiency was detected in the middle to basal region, as shown by the FV/FM and PhiPSII values. No chlorophyll fluorescence was detected in the apical part of the thallus, indicating that little or no photosynthesis takes place in these tissues. The lichen S. vesuvianum is homogeneously pale grayish green and chlorophyll containing cells are distributed along the thallus with maximum concentration in the middle region. In S. vesuvianum, the highest PS II efficiency was detected in the apical to middle region of the thallus, while the basal portion was found to have the lowest efficiency of primary photochemical reactions. Quenching analysis data confirmed the uneven patterns of primary photosynthetic processes within the thalli of these fruticose lichens.