With progress in science, new technologies open a window to answer the questions. Besides biological, serological and molecular methods, Next-generation sequencing (NGS) is one of the methods that changed our understanding of plant viruses, especially in the areas of identification, genome and transcriptome sequencing, evolution, taxonomy and quarantine programs. Recent methods make it possible to detect and identify all known and unknown viruses in a plant without the need for prior knowledge of the pathogen by the identify of total viral content and transcriptome of plant samples in healthy and disease conditions whearse ther are problems such as storage and analysis and interpretation of a large amount of data produced. Increases in the speed of detection of new viruses, viroids and hosts can prevent entering new viruses and viroids from foreign countries. More accurate and faster identification of plant viruses and their full effects on different hosts is one of the most important steps in disease management. In this article, we will review the applications of NGS in the diagnosis and detection of viruses, identification of diseases of unknown etiology and the study of host-pathogen interactions.