Turnip Mosaic Virus (TuMV) belongs to Potyvirus group in the Potyviridae family that it was reported from USA firstly. TuMV is distributed worldwide and it is known one of the most economically important plant virus around the world that has a wide host range over 300 plant species. MicroRNAs (miRNAs) are a class of non-coding RNAs, endogenous RNAs of 21–25 nucleotides (nts) in length. They play an important regulatory role in animals and plants by targeting specific mRNAs for degradation or translation repression. These small non-coding RNAs can contribute to the repertoire of host-pathogen interactions during viral infection. Viral infection can exert a profound impact on the cellular miRNA expression profile, and several RNA viruses have been reported to interact directly with cellular miRNAs and/or to use these miRNAs to augment their replication potential. The purpose of this study was to compare the expression of miRNAs in a control and TuMV infected Arabidopsis thaliana. To aim this research, small RNAseq from Arabidopsis leaves non-infected and infected by TuMV retrieved from GeneBank and the annotated miRNAs which produced in control and virus infection was separated, then results were compared by different next generation sequencing softwares. The results showed that expression of MIR165a/MIR165b was decreased after infection by TuMV compared with not infected plant. Reduction in the expression of miR165 conferred hypersensitivity to ABA during seed germination and post-germination seedling development. In addition, these miRNAs has an important role in auxin signaling and vascular development. In return, the MIR168a/MIR168b, MIR398b/MIR398c, MIR163 were over expressed when the plants infected by TuMV. Target genes of miR163 encode a family of small molecule methyltransferases involved in secondary metabolite biosynthetic pathways. Expression of miR163 could change target transcript and secondary metabolite profiles. The miR168-mediated feedback regulatory loop regulates Argonaute1 (AGO1) homeostasis, which is crucial for gene expression modulation, plant development, stress response and, signal transduction in plant. The miRNA398 directly linked to the plant stress regulatory network and regulates plant responses to oxidative stress, water deficit, salt stress, abscisic acid stress, ultraviolet stress, copper and phosphate deficiency, high sucrose and bacterial infection. Identification of the target genes of these miRNAs in Arabidopsis thaliana is in processing.