Plant viruses, viroids, and phytoplasma have been related to high crop production costs and pose a severe threat to agricultural output globally. The great genetic diversity of plant viruses, viroids, and phytoplasma makes it challenging to create markers that can identify every type of pathogen. The identification and detection of these infections have been transformed by molecular diagnostics, allowing for quick and precise diagnosis and the facilitation of efficient disease management techniques. Various molecular diagnostic techniques, consisting of polymerase chain reaction (PCR), reverse transcription PCR (RT-PCR), loop-mediated isothermal amplification (LAMP), and quantitative real-time PCR, are used to analyze plant viruses, viroids, and phytoplasma and treat plant illnesses. The information provided in this chapter will be helpful to researchers, plant pathologists, and others interested in plant disease management.