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A novel mycovirus named Fusarium oxysporum alternavirus 1(FoAV1) was identified as infecting <i>Fusarium oxysporum</i> strain BH19, which was isolated from a fusarium wilt diseased stem of <i>Lilium brownii</i>. The genome of FoAV1 contains four double-stranded RNA (dsRNA) segments (dsRNA1, dsRNA 2, dsRNA 3 and dsRNA 4, with lengths of 3.3, 2.6, 2.3 and 1.8 kbp, respectively). Additionally, dsRNA1 encodes RNA-dependent RNA polymerase (RdRp), and dsRNA2- dsRNA3- and dsRNA4-encoded hypothetical proteins (ORF2, ORF3 and ORF4), respectively. A homology BLAST search, along with multiple alignments based on RdRp, ORF2 and ORF3 sequences, identified FoAV1 as a novel member of the proposed family “<i>Alternaviridae</i><i>”</i>. Evolutionary relation analyses indicated that FoAV1 may be related to alternaviruses, thus dividing the family “<i>Alternaviridae”</i> members into four clades. In addition, we determined that dsRNA4 was dispensable for replication and may be a satellite-like RNA of FoAV1—and could perhaps play a role in the evolution of alternaviruses. Our results provided evidence for potential genera establishment within the proposed family “<i>Alternaviridae”</i>. Additionally, FoAV1 exhibited biological control of Fusarium wilt. Our results also laid the foundations for the further study of mycoviruses within the family “<i>Alternaviridae”</i>, and provide a potential agent for the biocontrol of diseases caused by <i>F. oxysporum</i>.