Influenza A virus H1N1 is the causative agent of the recent 2009 Swine flu or Swine influenza. The virus shows high rate of antibiotic resistance due to rapid mutation which leads to the production of new viral strains and hence, new vaccines are made to treat the new H1N1 variants. Neuraminidase plays an important biological role in this viral infection. It has been found that it has a major function at the final stage of infection when it cleaves sialic acid from cell surface and progeny virions facilitating virus release from the infected cells.The recent sequence of influenza A virus, A/California/04/2009(H1N1) for the protein, neuraminidase was selected for the study. Homology modelling was used to model the threedimensional structure of the neuraminidase protein using Modeller 9v6, Swiss Model and GENO3D. Energy minimization was performed by GROMACS and functional motifs were identified by the ProFunc server. CASTp server was used to determine the potential ligand binding sites. These ligand binding sites identified can thus provide an insight to design potential inhibitors in future.