On nutrient-poor rock surfaces, yeast-like black fungi (also called microcolonial fungi, MCF) may derive organic carbon either from the atmosphere or from interactions with other rock-inhabiting microorganisms. Interactions between free-living rock inhabiting heterotrophic fungi and phototrophic algae were investigated using axenic cultures. Five typical MCF strains were incubated with pure cultures of four lichen photobionts isolated from lichens growing in similar locations. After 2–12 months of combined cultivation, the fungal and algal colonies developed an overlapping structure involving both partners. Microscopic, histological and ultrastructural methods were used to investigate the changes that occur after prolonged contact. Histological analysis demonstrated changes in the spatial organisation of mixed colonies when in contact with each other. The branching of fungal hyphae was more pronounced in the vicinity of algal cells, thus increasing the potential contact surface. Photobiont cells were not changed in size, but a reduction of sporulation could be observed in some Trebouxia strains. Close cell wall contacts between fungal and algal cells were formed and mucilage accumulated at the contact places. The ability of MCF to form associations with potential photobionts present on rock surfaces was thus demonstrated for pure cultures in vitro.