Avian influenza viruses (AIV) have a wide host range in the avian metapopulation and, occasionally, transmission to humans also occurs. Surface water plays a particularly important role in the epidemiology of AIV, as the natural virus reservoir is found in aquatic wild birds.

The spread of viral diseases in eels is suggested to severely affect the European eel (Anguilla anguilla) panmictic population. The European Commission has initiated the Eel Recovery Plan (Council Regulation No. 1100/2007) to try to return the European eel stock to more sustainable levels within that measures eel restocking. However, scientific evidence evaluating the efficacy of stocking remains scarce. In addition, knowledge about the impact and contribution of eel stocking on the distribution of infectious diseases is insufficient. In this study, we aimed to investigate virus infections in batches of eels intended for restocking. We analysed samples of glass eels from certified fisheries and farmed European eels from different aquaculture farms. All analysed eels were purchased within a North Rhine Westphalian conservation program. Via a combination of cell culture and qPCR‐based techniques, we detected infections of glass eels with the rhabdovirus Eel Virus European X and anguillid herpesvirus 1 infections in farmed eels (10–15 cm).