Accurate detection and identification of plant pathogens are fundamental to plant pathogen diagnostics and thus plant disease management. The lack of rapid, accurate and reliable means by which plant pathogens can be detected and identified has been one of the main limitations in plant disease management and has prompted the search for alternative diagnostic techniques. The advent of enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) has caused a shift towards the use of molecular approaches in modern plant pathogen diagnostics. Nowadays, many techniques have been developed for the detection and identification of plant pathogens, each requiring its own protocol, equipment, and expertise. In addition, some of these techniques permit reliable quantification of the target pathogen as well, and supply the information required to estimate potential risks regarding disease development, spread of the inoculum, and economic losses. The major challenge at the moment is the development of multiplex assays that allow accurate detection and quantification of multiple pathogens in a single assay. In this chapter, we discuss recent advances in molecular plant pathogen diagnostics that are likely to impact future plant disease controlling and preventing strategies.