Emerging infectious diseases are actually of major concern worldwide. Most of them are zoonotic and their epidemiology must consequently be studied conjointly in humans and animals. We present here a long-term research program led in the Camargue. This area situated in the Rhone delta, crossroads of many birds‘ migration routes is a biodiversity hotspot. It appears vulnerable to disease emergence due to its key location and to the common use of wetlands by wild and domestic animals as well as humans. Since 2004, a health ecology program is led in the Camargue mainly focusing on Influenza A viruses. First, pathogen dynamics are studied in their wild reservoir. For example, a seasonal pattern of avian influenza A virus circulation in waterfowl was highlighted, an infection peak being generally observed in early fall, probably due to the massive arrival of young and possibly immunologically naive birds. Seasonality of avian Influenza viruses is currently studied in gulls. Second, pathogen transmission between wild and domestic birds is investigated. Interestingly, no highly pathogenic avian influenza virus was detected in wild birds of the region from 2006 to 2009 suggesting that migrating birds do not play an important role in the transmission of these viruses. On the other hand, the potential impact of domestic duck releases for shooting on avian influenza A viruses dynamics in wild waterfowl is currently studied. Finally, researches are led on pathogen exchanges between wildlife and humans. Antibio-resistant bacteria, similar to those circulating in humans in France, have been detected in gulls showing that they could be contaminated by human pathogens. This multidisciplinary program already proved that animal health, human health and ecology issues can be fruitfully linked to gain insight in the epidemiology of emerging pathogens. Besides, it highlights that long-term studies are needed to be able to face emerging health issues, rather than short-term studies limited to crisis periods that are necessarily insufficient.