| Summary: | Fungi constituting the <i>Entomophthora muscae</i> species complex (members of subphylum <i>Entomophthoromycotina</i>, phylum <i>Zoopagamycota</i>) commonly kill their insect hosts and manipulate host behaviors in the process. In this study, we made use of public transcriptome data to identify and characterize eight new species of mitoviruses associated with several different <i>E. muscae</i> isolates. Mitoviruses are simple RNA viruses that replicate in host mitochondria and are frequently found in more phylogenetically apical fungi (members of subphylum <i>Glomeromyoctina</i>, phylum <i>Mucoromycota</i>, phylum <i>Basidiomycota</i> and phylum <i>Ascomycota</i>) as well as in plants. <i>E. muscae</i> is the first fungus from phylum <i>Zoopagomycota</i>, and thereby the most phylogenetically basal fungus, found to harbor mitoviruses to date. Multiple UGA (Trp) codons are found not only in each of the new mitovirus sequences from <i>E. muscae</i> but also in mitochondrial core-gene coding sequences newly assembled from <i>E. muscae</i> transcriptome data, suggesting that UGA (Trp) is not a rarely used codon in the mitochondria of this fungus. The presence of mitoviruses in these basal fungi has possible implications for the evolution of these viruses.
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