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Background:Avian influenza viruses (AIVs) have been identified from more than 100 different species of wild birds around the globe. Wild migratory birds can act as potential spreaders for AIVs to domestic birds between different countries. Egypt is situated on important migratory flyways for wild birds between different continents. While much is known about circulation of zoonotic potential H5N1 and H9N2 AIVs in domestic poultry in Egypt, little is known about the pivotal role of migratory birds in the maintenance and transmission of the viruses in Egypt. Methods: Targeted AIV surveillance has been conducted in 2017 in different wetlands areas in North and East Egypt. Results: AIV of subtype H5 was detected in two bird species. In addition, a novel reassortant strain of the H6N2 subtype was identified which reveals the continuous risk of new influenza virus(es) introduction into Egypt. This novel virus possesses a reassortant patt originating from different AIV gene pools. Conclusions: Intervention control strategies should be performed to minimize the possible contact of domestic birds with wild birds to lower the risk of virus transmission at this interface. In addition, constant monitoring of AIVs in migratory birds is essential in the early detection of influenza virus introduction into Egypt.