The current state of scientific researches in lichen microbiology was reviewed. Analysis of the literature revealed the main areas and fundamental issues which refer to investigation of microbial consortia in lichen bodies. Special attention was focused on analysis of the prokaryotic community which plays a structural and functional role and is involved in metabolism and regulation of activity of the lichen symbiosis as a whole. In the review, for the first time the information on the yeast community, of which some members do not occur presently in other environmental substrates, was summarized. The data on the protozoa inhabiting lichen thalli were also provided. The reviewed literature enabled us to consider the growing and decaying thallus as a complex ecosystem with specific levels of regulation of abundance, taxonomic diversity, and activity of the members of five kingdoms: fungi, plants, protozoa, eubacteria, and archaea.