Abstract: To discover and identify the mycovirus sources in Corynespora cassiicola strains, high-throughput sequencing and mycovirome analysis were used to discover and identify the mycoviruses in eleven C. cassiicola strains isolated from tobacco leaves in China. Based on the obtained viral sequence data, structural protein prediction and phylogenetic analyses were performed, and the infections of different viruses in the test strains were clarified. The results showed that: 1) These strains carried a total of five mycoviruses, including three double-stranded RNA (dsRNA) viruses, one positive-sense single-stranded RNA (+ssRNA) virus and one negative-sense single-stranded RNA (-ssRNA) virus. 2) Coding protein alignments and phylogenetic analyses indicated that two of these five viruses belonged to Totiviridae, while the other three belonged to Partitiviridae, Narnaviridae, and Aspiviridae, respectively. 3) RT-PCR detection results showed that the virus carrying rate of these strains was 64%, and two strains had mixed infection of the viruses.