Global mollusc production is continuously increasing and reached 12.8 million tonnes in 2004 representing 28.2 percent of the total world production valued at US$ 9.4 billions. However, cultivated molluscs may suffer from severe mortality outbreaks. Among the possible causes is the occurrence of infectious diseases due to a variety of pathogens including protozoan parasites, bacteria and viruses. Preventing and controlling diseases has become a priority for aquaculture sustainability. However, molluscs are unique in terms of health management. Molluscs like other invertebrates, lack a true adaptative immune system. Vaccination can not be used to protect them against pathogens. Moreover, molluscs are usually reared in the open sea which strongly limits the use of drugs. Finally, pathogen transfers via movements of aquatic organisms appear to be a major cause of epizootics. In this context, a better knowledge of pathogen taxonomy and the development of molecular diagnostic tools are needed. The taxonomic history of various mollusc pathogenic agents has known controversy last decades. However, molecular biology in recent years allowed clarify some points. Molecular detection assays for pathogens infecting molluscs are being developed at an increasingly rate. Molecular techniques are now moving from development in specialised laboratories for research purposes, to routine application and are expected to be increasingly used in pathogen monitoring programs. The DNA based diagnosis tools need however validation, specificity definition and further development.