In efforts to limit transboundary movement of pathogens and reduce the economic and socioeconomic impact of disease in aquaculture, there is considerable scope for more effective use of DNA-based methods of pathogen detection. These technologies offer rapid results with potentially high sensitivity and specificity, at relatively low cost. However, few, if any, of the available tests have been assessed appropriately against other diagnostic methods or standardized and validated for specified applications. Implementation of standardized practices that produce reliable, useful and comparable data will require a significant investment in research, training and infrastructure development. This review recommends the development of programmes of managed cooperative research to assist more effective use of DNA-based detection tests, focusing on improving the knowledge base by identification of new and emerging pathogens, relating pathogens in the Asia region to those described elsewhere, and defining the extent of genetic variation between related pathogens. The review also recommends the development of a laboratory accreditation programme in order to achieve standardization of sampling methods and test procedures complementary to the activities of the International Office of Epizootics (OIE) in obtaining internationally agreed test standards for molecular diagnostic technologies.