A recently emerged novel influenza A (H1N1) virus continues to spread globally. The pandemic caused by this new H1N1 swine influenza virus presents an opportunity to analyze the evolutionary significance of the origin of the new strain of swine flu. Our study clearly suggests that strong purifying selection is responsible for the evolution of the novel influenza A (H1N1) virus among human. We observed that the 2009 viral sequences are evolutionarily widely different from the past few years' sequences. Rather, the 2009 sequences are evolutionarily more similar to the most ancient sequence reported in the NCBI Influenza Virus Resource Database collected in 1918. Analysis of evolutionary rates also supports the view that all the genes in the pandemic strain of 2009 except NA and M genes are derived from triple reassorted swine viruses. Our study demonstrates the importance of using complete-genome approach as more sequences will become available to investigate the evolutionary origin of the 1918 influenza A (H1N1) swine flu strain and the possibility of future reassortment events.