Background: The aim of the study was to explore the ecological diversity of wild birds in Siberia, which are the natural reservoir of avian influenza virus (AIV). Methods: Cloacal swabs and intestinal fragments were collected from wild migratory birds from 2007-2014. Isolated viruses were grown in the allantoic cavity of embryonated chicken eggs. The presence of virus was determined using hemagglutination assays. Primary identification and subtyping of influenza viruses was confirmed by RT-PCR. Results: A total of 2300 samples obtained from wild migratory birds of 8 orders were collected and tested. Influenza was detected in 185 birds of 3 orders. Species of family Anatidae (order Anseriformes) such as European Teal (Anas crecca), Garganey Teal (A. querquedula), and Shoveler (A. clypeata) play the main role in AIV circulation in the south of Western Siberia. The proportion of viral carriers among waterfowl ranged from 5.6 to 20% in 2007-2014. The order Charadriiformes had lower virus isolation rates of not more than 1.4%. Conclusions: Wild migratory waterfowl of orders Anseriformes and Charadriiformes are the main reservoir of AIV in the south of Western Siberia. This area plays a key role in persistence, evolution, and geographical distribution of avian influenza. © 2017 The Author(s).