Surveillance of mollusc diseases is routinely performed by histology and PCR. Efforts made in research and development of DNA-based diagnostic methods currently offer a broad panel of probes and tests. These methods have the theoretical advantages of high sensitivity and high specificity and possible rapid screening of molluscs for the presence of a targeted pathogen. However, validation and standardisation of these tests are still needed. In recent years, the European Union Reference Laboratory (EURL) for mollusc diseases has developed and validated a range of duplex Taqman® PCR assays aiming at facilitating the detection of bivalve pathogens notifiable to the EU. These assays offer good performances and allow better monitoring and investigation of the epidemiology of these different pathogens. Complementary to these PCR assays, new diagnostic approaches based on the use of passive sensors, Magnetic Beads (MBs), electrochemical biosensors, MALDI-TOF MS or Next Generation Sequencing (NGS) have been developed and tested notably in the context of the European project H2020 VIVALDI. The interest of these tools to better detect, characterise and monitor known pathogens is presented and discussed. These new developments will require further assessment, standardisation and validation before being available for routine diagnostics. Additionally, they will certainly not replace but rather complement diagnostic tools currently used to ensure alertness to emerging diseases.