The phytotoxic effects of the lichen secondary metabolite-usnic acid on cultures of free living alga-Scenedesmus quadricauda (UTEX 76) and aposymbiotically grown lichen photobiont Trebouxia erici (UTEX 911) were assessed. We found a relatively strong inhibition effect of usnic acid on the growth of alga Scenedesmus, accompanied by an increase of cell size, an alteration of assimilation pigment composition, followed by strong degradation of chlorophyll a, a decrease of chlorophyll a fluorescence, and an increase of reactive oxygen species in the cells. The content of soluble proteins remained a stable parameter. Phytotoxicity of usnic acid on cultures of Trebouxia photobiont was significantly lower. Usnic acid in lichens may act as an allochemical that controls the division of photobiont cells, thereby regulating the balance between the photobiont and mycobiont forming thallus. Higher tolerance to usnic acid in Trebouxia cultures may be an adaptation resulting from the long term co-evolution of these algae with fungi that produce secondary metabolites.