Influenza virus infections cause severe illness worldwide. Vaccination reduces the morbidity and mortality of influenza. The efficacy of vaccines varies due to antigenic differences between the circulating influenza strains and the vaccine. Neuraminidase inhibitors are effective for prophylaxis and treatment of influenza infections, and the emergence of drug resistant mutants is an important challenge. Full-length nucleotide and deduced amino acid sequences of the hemagglutinin and neuraminidase genes of three 2009 pandemic influenza A/H1N1 isolates were compared with the vaccine strain and some strains from different countries. Phylogenetic analysis for hemagglutinin and neuraminidase showed they were related to their vaccine strain, with an average of 99.56 and 99.53% sequence identity, respectively. No genetic indication of resistance to neuraminidase inhibitors was found. Although genomic analysis of hemagglutinin and neuraminidase genes of Iranian strains in comparison to the corresponding vaccine strain revealed some mutations, none of these were identified in functionally important receptor-binding sites.