The suddenly global outbreak of 2009 H1N1 Flu reminds human being the danger and severity of influenza virus. The gene of the new strain come from five different influenza viruses: North American swine influenza, North American avian influenza, human influenza, and two swine influenza viruses typically found in Eurasia. The recombination of gene in virus evolvement makes it more and more important to understand the evolutionary characteristics of influenza. Hemagglutinin (HA), embedded on the surface of influenza virus, is one of two virally-coded integral envelope proteins of the virus. The three primary functions of hemagglutinin (HA) include receptor binding, membrane fusion, and antigenic variation. Study of HA structure and its evolutionary mechanism is crucial to fully understand influenza virus. In the first chapter, a study of diversifying selective pressure on influenze B virus hemagglutinin was reported. All the positively selected sites were located in the four epitopes (120-loop, 150-loop, 160-loop and 190-helix) of HA, and all of them have been identified in previous studies. This supports a predominant role of antibody selection in HA evolution. In the second chapter, we studied positive selection analysis of 2009 HINT Flu. Among a subgroup of human A(H1N1) HAs between 1918∼2008, we found strong diversifying (positive) selection at HAI 156 and 190. We also analyzed the evolutionary trends at HAI 190 and 225 that are critical determinants for receptor-binding specificity of A(H1N1) HA. Additional analysis of directional selection was also employed for H1N1 gene data.