Plants in field conditions are subjected to a range of biological and environmental stresses, with plant diseases induced by phytopathogens posing a significant risk to global food security. Consequently, the development of effective diagnostic technologies for early plant disease detection is imperative to ensure agricultural sustainability and safeguard the world’s food supply. The advent of molecular diagnostics has revolutionized the diagnosis and profiling of plant viruses, viroids, and phytoplasma, offering swift and precise methods for infectious agent identification, quantification, and characterization. Therefore, this chapter has been aimed to give an in-depth look at a multitude of molecular tools employed in the detection and identification of plant viruses, viroids, and phytoplasma. Molecular techniques such as polymerase chain reaction (PCR), quantitative PCR (qPCR), recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), DNA microarray, etc. enable the precise and highly sensitive detection of these phytopathogens, even in asymptomatic plants. In addition, high-throughput sequencing (HTS) and metagenomics provide an extensive view of the pathogen diversity in a given specimen. The use of molecular diagnostics in plant virus, viroid, and phytoplasma management can aid in the early identification and swift reaction to outbreaks, ultimately leading to better disease management and crop protection.