Plant diseases caused by plant pathogenic viroids are a serious threat to agricultural production in the world. Recently, initiatives initiated through molecular biotechnology have been effective strategies for the prevention and control of plant-infecting viroids. Sequencing of the new generation examines the direct and indirect interactions of viroids with host factors, and using this technology, changes in the proteome and host transcripts during infection with viroids are identified, and by examining the interactions between viroids and plants, Useful strategies to combat these pathogens. Recent advances in targeted DNA or RNA editing with CRISPR/Cas related systems are also very attractive tools that can be used in plant protection. In this review article, we review the progress of CRISPR/Cas systems to date against plant pathogenic viroids, and the use of these methods in controling some plant viroids by targeting specific sequences or genes in these factors will be discussed.