Brazil is the leading country in the use of the entomopathogenic fungus Metarhizium anisopliae against agricultural pests. Very little information has been documented about the diversity and the impact of mycoviruses on M. anisopliae compared to M. robertsii and M. brunneum. This study reports the discovery of mycoviruses associated with native Brazilian Metarhizium spp. strains from the entomopathogen collection of the University of São Paulo, including strains used for mass-production of aerial conidia in sugar-alcohol factories to meet their own demand for controlling sugarcane spittlebugs and used in commercial mycoinsecticides. We also investigated the potential effects of viral infection on the biological traits of some of these strains. Viral-like double-stranded RNA (dsRNA) was found in 61% of the 36 Metarhizium spp. strains analyzed and showed a large variation of different electrophoretic banding patterns consisting of 2 to 8 dsRNA bands in polyacrylamide gels (PAGE). No dsRNA was detected in any of the strains from commercial products used in this study. Efforts to “cure” strains with dsRNA revealed that the inhibitor of protein synthesis cycloheximide was not efficient in eradicating dsRNA viruses from Metarhizium spp. strains. Some dsRNA segments of M. anisopliae ESALQ 26 were lost following hyphal tip subculturing. The dsRNA-variants of M. anisopliae strains ESALQ 866, ESALQ 1256 and ESALQ 1595 were healed after either monoconidial or hyphal tip subculturing. Single spore cultures of M. anisopliae ESALQ 1256 exhibited significant differences in vegetative growth, conidia production, and virulence against Tenebrio molitor larvae, although these differences were not linked with dsRNA. Moreover, fungal variants free of or positive for dsRNA had similar heat and UV tolerance responses. Our results suggest that viral-like dsRNA are very common among Brazilian M. anisopliae strains, but there is sparse evidence that these mycoviruses are harmful to fungal biological traits.