In this study we investigated the “virome” of Macrophomina phaseolina (MP), an important and polyphagous phytopathogenic fungus causing “charcoal rot” disease in soybeans. In order to characterize community of viruses with RNA genomes in this host, total of 35 MP isolates collected from soybean fields in Mississippi were isolated in pure culture on PDA plates, submitted to dsRNA extraction, library preparation and subsequent custom-based pair-end Illumina sequencing. The majority of MP isolates examined in this study revealed presence of complex patterns of high molecular weight dsRNA molecules, suggestive of multiple infections. Presence of viruses was confirmed by transmission electron microscope observations of putative viral particles in partially purified and negatively-stained preparations from several dsRNA-containing fungal isolates. Computer-based assembly of Illumina-generated raw sequence data resulted in thousands of virus-specific contigs of different size. In silico analyses revealed presence of several viruses recently reported from this hosts, along with dozens of new ssRNA and dsRNA viruses belonging to currently recognized genera and/or families. In addition to characterization of new viruses, we completed genome sequences of several known viruses and investigated their population structure and distribution in studied MP isolates. Several viruses characterized in this work differ from known viruses in their genomic properties and may represent founder members of new taxa. These results further the knowledge about general mycovirus diversity.