Mycoviruses have been detected from all four classes of fungal endophytes. The virus species richness is probably extremely high in endophytes. The incidence and diversity of mycoviruses may be affected by transmission modes, virus-fungus-plant interactions, and endophyte population structures. Endophyte viruses are unlikely to be strong antagonists to their fungal hosts and can clearly play mutualistic roles in the multiplex symbioses with endophytes and plants under some environmental conditions. A better understanding of fungal endophyte viruses will help prospects of future applications for sustainable agriculture.