Anguilla anguilla, A. japonica and A. rostrata are the most fished and consumed eel species. However, these species are Critically Endangered, Endangered and Endangered respectively. A combination of factors is thought to be responsible for their decline including fisheries, climate change, habitat destruction, barriers to migration, pollution and pathogens. Among them, viruses, bacteria and parasites are causing weakening of wild eels and serious economic losses for fishermen and eel farmers. Early detection of pathogens is essential to provide appropriate responses both for conservation reasons and to limit economic losses. Classic diagnosis approaches are time consuming and invasive and usual treatments e.g. antipathogenic substances are becoming obsolete because of pathogen resistance and environmental impact problems. The need for early and noninvasive diagnostic methods as well as effective and environmentally friendly treatments has increased. Vaccine development and diet supplementation have known a growing interest since their use could allow prevention of diseases. In this review, we summarize the main pathogens-viruses, bacteria and parasites-of the three northern temperate eel species, the methods used to detect these pathogens, and the different treatments used. We discussed and highlighted the need for non-invasive, rapid and efficient detection methods, as well as effective and environmentally friendly treatments for both conservation and aquaculture purposes.