The H1N1 subtype of Influenza A virus is the causative agent of swine flu. The 2009 outbreak caused by subtype H1N1 in humans is due to transfer of Swine Influenza Virus from pig to human. Thus to analyze the origin of this novel virus we compared the 42 nucleocapsid sequences of H1N1 viruses of different origins. Phylogenetic analysis of these sequences was carried out along with bootstrap analysis of 100 replicates. The phylogenetic tree constructed revealed that Indian H1N1 strain showed the highest homology with Iowa H1N1 strain and also with Wisconsin H1N1 strain. Further the H1N1 strains analyzed using NP sequences of different Indian origins showed highly close sequence similarity. Hence, in future this study will be helpful for knowing the taxonomy and evolution of influenza viruses.