Microorganisms, including those genetically modified (GMOs), are increasingly being released deliberately into the environment for different purposes. One major interest is the use of antagonistic organisms for biological control of pests and plant diseases. Both in the development of biocontrol agents and their later risk assessment and product approval, there is a need for methods that facilitate monitoring of such introduced microorganisms. This book particularly addresses the various approaches for monitoring introduced fungi and the current status of techniques which may be relevant to use are described. Such techniques include marker genes and other DNA-based techniques, serology using polyclonals or monoclonals, the use of enzymes or secondary metabolite profiles, and “electronic noses’ as well as more traditional methods like dilution plating.