Viruses infecting microorganisms includes all viruses that infect bacteria, archaea and single-celled eukaryotes, and fungi. Before the discovery of antibiotics, bacterial viruses, also called as bacteriophages were initially studied for their bactericidal properties to treat infectious diseases. Apart from this, fungal viruses (mycoviruses) appear to be ubiquitous in nature as well, as most fungal lineages show evidence of viral infections. Virus-mediated lysis of fungal hosts is exceptionally rare, however, and most mycoviruses establish persistent, asymptomatic infections of their hosts. The significance of mycovirus infections therefore may lie in subtle modulations of host gene regulation but also can affect host secretion of toxins, hypovirulence, and thermotolerance. During the recent past, these viruses were used as tools to understand the molecular mechanisms of cellular processes. Over the past two decades, the advancement of viral ecology has led to the realization that viruses of microbes are the most abundant biological entities on earth and play a major regulating role in ecosystems. They are considered as chief contributors to horizontal gene flow and drivers of evolution. Phage based biocontrol and mycoviruses induced hypovirulent strains is an exciting rediscovered field of disease management. They are natural components and hence can be fitted in organic farming strategies. Thus, the viruses of microorganisms play a important role in evolution, ecology, plant health and biocontrol.