The use of electron microscopy, both transmission and scanning, provides reliable and accurate methods for detecting phytoplasmas in plants. Our understanding of these pathogens, their morphology, development, and intracellular location in plants and insect vectors has been greatly increased through the use of these instruments. Development of techniques such as immunolabeling, cryofixation with freeze substitution or plunge freezing with direct transfer to the microscope stage, together with advances in instrumentation is enabling us to study these pathogens under conditions close to their native state. The visualization of fine detail and ultrastructure, using modern and established techniques, can only be appreciated by the magnification and spatial resolution offered in the electron microscopes. Now that the full sequencing of four phytoplasma genomes (to date) has been achieved, electron microscopy can play an important role in identifying and understanding specific gene functions.