Introduction: Influenza is a contagious acute viral disease of the respiratory tract that causes fever, headache, muscle aches and cough. One of the unique features of influenza virus is antigenic variation in viral protein neuraminidase (NA) which causes emergence of new virus variants. NA is responsible for the release and spread of progeny virions. Due to the continuous changes of NA genes, vaccine strains must be re-selected annually. Methods: Complete NA amino acid sequences of 97 strains circulating from 2006 to 2013 in Iran were downloaded from NCBI. The sequences were edited and classified by the year of isolation and their diversity and important changes as well as changes in the predicted ligand binding sites and their resistance to anti-NA drugs, were analyzed. Bioinformatics software such as MEGA6.0, BioEdit, DNAsisMAX and DNAstar were used for the sequence alignments and phylogenetic analyses. Web-based analysis such as SWISS-MODEL, Phyre2 and 3DLigandSite were used for evaluation of the second and third protein structures and prediction of the ligand binding sites. Results: The results showed that 2009 could be considered as an important transition year which caused to classify the isolates into two different distinct groups. This shows the importance of changes made during possible mutations in the genomic structure of the virus which have made it antigenically different from the previous years. Anti-NA drug resistance was observed in 2009. This pandemic strain has become dominant in the following years and is used as a standard vaccine strain from 2010 onwards. Conclusion: The results obtained in this study can aid in better understanding of the antigenic evolution of H1N1 influenza viruses and can potentially accelerate the selection of the vaccine strains.