BACKGROUND: The H9N2 subtype of avian influenzaviruses (AIVs) has been isolated in multiple avian species inmany European, Asian, African and American countries. Sincethe first outbreak of H9N2 virus in Iran in 1998, this virus haswidely circulated throughout the country, resulting in majoreconomic losses in chicken flocks. Several amino acids in thevirus ribonucleoprotein (RNP) complex including the nucleoprotein(NP) and polymerase (PB2, PB1 and PA) proteins areassociated with host range and virulence. OBJECTIVES: Our aimwas to understand the molecular characterization of RNPcomplex proteins of Iranian H9N2 subtype isolates. METHODS:The full length nucleotide sequences of RNP complex genes oftwo strains designated as Ck/IR/ZMT-101/98 and Ck/IR/EBGV-88/10 were amplified and sequenced. RESULTS: The phylogeneticanalysis revealed that both strains were located indifferent sub-lineages. However, based on the genetic similarities,PB1, PAand NP genes of Ck/IR/EBGV-88/10 strain had aclose relationship with a H7N3 subtype strain, isolated fromPakistan. Most positions of RNP proteins contained amino acidstypical of avian determinants of host range. The results showedthat the Iranian RNP complex genes have undergone geneticreassortment. CONCLUSIONS: Continuous AIV monitoring inpoultry industry would help to obtain more information aboutgenetic variation of H9N2 viruses and possible emergence ofvirulent and/or pandemic viruses.