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Cloacal and tracheal swab-samples were collected from commercial farms, backyards and live market birds (LBM) to identify the potential existence and genetic drifts of avian influenza subtypes (AI) H5 and H9 that are circulating among bird species in Egypt. The results revealed that, one sample out of 50 samples of chicken commercial farms was positive for the isolation of subtype H9N2 [KC699549, Influenza A virus: A/chicken/Egypt/VRLCU-R33/ 2012(H9N2)]; from Sharkeia province. Two samples out of 20 samples of Backyard ducks were positive for the isolation of 2 subtypes H5N1; [KC699547, Influenza A virus: A/duck/Egypt/ VRLCU-R11/2012(H5N1), ''backyard duck''] from El-Fayoum province and the other from Giza province [A/duck/Egypt/VRLCU-R28/2012(H5N1), ''backyard duck'']. Analysis of haemagglutinin (HA) and the phylogenetic tree of the isolated viruses (H5N1) were fallen within the clade 2.2.1.1. Antigenic cartography for the isolated Egyptian H9N2 AI virus can intuitively be of group-B. The number of mutations in the amino acid sites (33, 47, 65, 90, 92, 143, and 150) and the Long Branch observed in the phylogenetic tree may suggest a rather long evolution period. The sequenced H9N2 Egyptian virus in the study was closely related to the previous Egyptian isolates. ª 2014 Production and hosting by Elsevier B.V. on behalf of Faculty of Veterinary Medicine, Cairo University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/ licenses/by-nc-nd/3.0/).