Black, rock inhabiting fungi (RIF) are polyextremotolerant, oligotrophic organisms which colonize bare rocks and are specialized to grow in niches precluded to other microorganisms in the harshest environments. In many cases RIF share this environment with green algae and cyanobacteria forming subaerial biofilms; some of them have also been found to be associated with lichen thalli. The RIF genus Lichenothelia is of particular interest because it includes lichen parasites and species which are loosely associated with algae or grow independently on rocks. Here, in vitro culture experiments studied the development of three Lichenothelia species when co-cultured with two different lichen photobionts on growth media differing in nutrient content. The growth rates of these fungi were statistically evaluated and the structure of the mixed cultures was analyzed by light and scanning electron microscopy. The results show that the presence of algae neither influence the growth rate of fungi nor the formation of any lichen-like structure; tight contacts between the hyphae and the algal cells were also not detected. Since multiple trials were carried out on well characterized species of microcolonial fungi and the methodological procedures were established, standardized and coupled with morphological analyses, this approach proves suitable for future investigations on fungal-algal interactions in other systems.