ABSTRACTWheat sharp eyespot caused byRhizoctonia cerealisis primarily a severe threat to worldwide wheat production. Currently, there are no resistant wheat cultivars, and the use of fungicides is the primary method for controlling this disease. Elucidating the mechanisms ofR. cerealispathogenicity can accelerate the pace of the control of this disease. Long intergenic noncoding RNAs (lincRNAs) that function in plant-pathogen interactions might provide a new perspective. We systematically analyzed lincRNAs and identified a total of 1,319 lincRNAs inR. cerealis. We found that lincRNAs are involved in various biological processes, as shown by differential expression analysis and weighted correlation network analysis (WGCNA). Next, one of nine hub lincRNAs in the blue module that was related to infection and growth processes,MSTRG.4380.1, was verified to reduceR. cerealisvirulence on wheat by a host-induced gene silencing (HIGS) assay. Following that, RNA sequencing (RNA-Seq) analysis revealed that the significantly downregulated genes in theMSTRG.4380.1knockdown lines were associated mainly with infection-related processes, including hydrolase, transmembrane transporter, and energy metabolism activities. Additionally, 23 novel microRNAs (miRNAs) were discovered during small RNA (sRNA) sequencing (sRNA-Seq) analysis ofMSTRG.4380.1knockdown, and target prediction of miRNAs suggested thatMSTRG.4380.1does not act as a competitive endogenous RNA (ceRNA). This study performed the first genome-wide identification ofR. cerealislincRNAs and miRNAs. It confirmed the involvement of a lincRNA in the infection process, providing new insights into the mechanism ofR. cerealisinfection and offering a new approach for protecting wheat fromR. cerealis.IMPORTANCERhizoctonia cerealis, the primary causal agent of wheat sharp eyespot, has caused significant losses in worldwide wheat production. Since no resistant wheat cultivars exist, chemical control is the primary method. However, this approach is environmentally unfriendly and costly. RNA interference (RNAi)-mediated pathogenicity gene silencing has been proven to reduce the growth ofRhizoctoniaand provides a new perspective for disease control. Recent studies have shown that lincRNAs are involved in various biological processes across species, such as biotic and abiotic stresses. Therefore, verifying the function of lincRNAs inR. cerealisis beneficial for understanding the infection mechanism. In this study, we reveal that lincRNAs could contribute to the virulence ofR. cerealis, which provides new insights into controlling this pathogen.