It is a research direction under rapid development to monitor aquatic systems by environmental DNA（eDNA）that，with rapid，economic and non-invasive sampling plan，is more suitable for disease detection and monitoring of rare or precious aquatic animals or wild animals that were difficult to be sampled. In the paper，based on the documents for discussion issued by Aquatic Animal Committee（AAC），World Organization for Animal Health（WOAH），the collection and disposal of samples in aquatic animal disease surveillance by eDNA，the validation and confirmation of the method，and its applicability in the surveillance were reviewed，and it was proposed that the positive result might be an appropriate criteria to determine any suspicious cases，although eDNA was not suitable to support any free declaration of WOAH listed animal diseases because it failed to obtain any accurate estimates of diagnostic performance. It was recommended that，with its advantages，eDNA could be used in aquatic animal disease surveillance in entry-exit establishments and temporary quarantine facilities holding aquatic animals intended for human consumption，breeding and ornamental purposes，especially used in the surveillance on the diseases of special high-value aquatic animals and aquatic animals living on large water surfaces.