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In the present study, sixteen novel RNA mycoviruses co-infecting a single strain of <i>Rhizoctonia zeae</i> (strain D40) were identified and molecularly characterized using metatranscriptome sequencing combined with a method for rapid amplification of cDNA ends. The fungal strain was isolated from diseased seedlings of sugar beet with damping-off symptoms. Based on genome analysis and phylogenetic analysis of amino acid sequences of RNA-dependent RNA polymerase, the sixteen mycoviruses associated with strain D40 contained three genome types with nine distinct lineages, including positive single-stranded RNA (<i>Hypoviridae</i>, <i>Yadokariviridae</i>, <i>Botourmiaviridae</i>, and <i>Gammaflexiviridae</i>), double-stranded RNA (Phlegiviridae, <i>Megabirnaviridae</i>, Megatotiviridae, and Yadonushiviridae), and negative single-stranded RNA (<i>Tulasviridae</i>), suggesting a complex composition of a mycoviral community in this single strain of <i>R. zeae</i> (strain D40). Full genome sequences of six novel mycoviruses and the nearly full-length sequences of the remaining ten novel mycoviruses were obtained. Furthermore, seven of these sixteen mycoviruses were confirmed to assemble virus particles present in the <i>R. zeae</i> strain D40. To the best of our knowledge, this is the first detailed study of mycoviruses infecting <i>R. zeae</i>.