The earliest evidences on circulation of Avian Influenza (AI) virus on the Iranian poultry farms date back to 1998. Great economic losses through dramatic drop in egg production and high mortality rates are characteristically attributed to H9N2 AI virus. In the present work non-structural (NS) genes of 10 Iranian H9N2 chicken AI viruses collected during 1998-2007 were fully sequenced and subjected to a phylogenetic analysis. The observations proved allele A was the single-detectable type of the NS gene within the studied isolates. All the examined Iranian isolates fell into the Korean sublineage with a relatively broad sequence homology (91.6-98%) in nucleotide construction of the NS genes. The motif for PDZ ligand recognition of the group one isolates was either EDEV (N=6) or ESEV (N=1) While all viruses as group two contained a PL motif “KSEV” (N=3). The present work provides useful epidemiological data at molecular level on source and contemporary evolution of H9N2 virus population in Iran.