Almost all plants live in interactions with fungi, where they express different lifestyles ranging from mutualism (beneficial for both partners) through commensalism (beneficial for the microbe, while the host species is neither positively nor negatively affected) to parasitism (the host is noticeably harmed or deprived at the expense of the fungus). Mutualism represents a balanced stage of plant/microbe interactions. However, depending on the partner combination, the genetic constitutions of both partners, the developmental stage and the life-history of the symbiosis, the physiological status of both partners, the colonization pattern of the host, the ability of the microbe to produce toxins and of the host to defend them, the evolutionary status of the symbiosis, environmental and habitat-specific conditions and the stress situation, a mutualistic interaction can become unstable and shift towards commensalism or parasitism. Genetic studies with mycorrhizal and endophytic fungi discovered genes which are crucial for determining a beneficial symbiotic stage. Recent progress in this field is summarized in this review. In addition, the interaction of the endophytic fungus Piriformospora indica with Arabidopsis as a novel model system in this field is introduced.