Advanced molecular genetic techniques enhance our capabilities to identify and characterize microbial pathogens, resulting in accurate testing for pathogen identification, sub-species-level DNA fingerprinting, pathogen-load testing and disease spread monitoring. These applications are instrumental to the study of plant disease epidemiology, so that adequate control measures can be accordingly implemented. In this chapter, a survey of the most popular DNA profiling techniques is presented together with some of the newer and most discriminating molecular methods. Combinations of different analytical techniques are also proposed as a useful approach for low throughput bioassays. Advantages and disadvantages of each single test are taken into account and key issues (sampling, validation, large-scale testing, etc.), encountered in the practical application of these assays, are discussed. An outline of emerging high-throughput molecular technologies expected to improve diagnostic approaches and aid disease management is also provided.