Lichens were traditionally considered as a remarkable assemblage of fungi with unicellular phototroph (algae or cyanobacteria) that have converged on similar symbiotic strategies. However, this view of lichens has recently been reconsidered by findings of miscellaneous associated microbes colonizing on or within the thallus causing no apparent effect. This hidden diversity includes filamentous fungi, lichen-inhabiting yeasts, as well as various prokaryotic bacteria. Despite these endothallic and exothallic organisms do not belong to constant lichen symbionts, they usually play important roles in lichen biology by participating in the lichen metabolism, regulating water relations, affecting thallus architecture, and being involved in the degradation processes. However, it is often difficult to understand microorganismal input and uptake and therefore determine their symbiotic outcome due to the complexity of lichen symbiosis. In this chapter, diversity and biological role of usually neglected or overlooked lichen microbial consortia are reviewed and their possible biotechnological application is discussed.