Members of the fungal genus Hypoxylon of the family Xylariaceae are known to produce secondary metabolites with significant chemical diversity. There are more than 200 species in the genus, including the filamentous fungus Hypoxylon fendleri. To the best of our knowledge, there have been no reports of mycoviruses in H. fendleri. In this study, a novel mycovirus, designated “Hypoxylon fendleri mitovirus 1” (HfMV1), was isolated from this fungus. The genome of HfMV1 is 2850 nt in length with a G + C content of 36% and contains a large open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRp). BLASTp analysis revealed that the RdRp domain of HfMV1 had 28.30–50.90% sequence identity to those of members of the genus Duamitovirus and had the highest identity (50.90%) to Fusarium graminearum mitovirus 2-2 (FgMV2-2). Phylogenetic analysis further indicated that HfMV1 is a member of the genus Duamitovirus of the family Mitoviridae. This is the first report of a mycovirus in H. fendleri.