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MicroRNAs regulate plant responses to fungal infections and immunity. In this study, miRNAs were identified in six rice cultivars during a <i>Rhizoctonia solani</i> Kühn AG1-IA infection using a deep sequencing approach. Known and novel miRNAs were analyzed in these rice cultivars, and a set of fungal infection/immunity-associated miRNAs and target genes were quantified by reverse transcription (RT)-qPCR in six rice cultivars. Additionally, the relative expression of these miRNAs was analyzed in different time points of the infection, wild species of rice, and in response to different strains of <i>R. solani</i>. Osa-miR1320-5p showed preferential expression during the fungal infection in all the six rice genotypes, while Osa-miR156d, Osa-miR159b, Osa-miR820c, and Osa-miR1876 were differentially regulated in susceptible and resistant genotypes. A greater degree of downregulation of miRNAs was observed during the initial time points of infection (24–72 h), suggesting a maximum molecular activity of rice-<i>R. solani</i> interaction and resistance response of the host during the early phase of infection. After <i>R. solani</i> infection, the expression of Osa-miR820c and Osa-miR156d was downregulated in <i>Oryza rufipogon, O. alta, O. latifolia,</i> and <i>O. minuta</i>, while Osa-miR397b was downregulated in all the wild rice species except <i>O. officinalis</i>. This study provided comprehensive information on the repertoire of miRNAs expressed in six sheath blight disease-susceptible and resistant <i>indica</i> and aus rice cultivars.