The overall aim of my study is to address fundamental questions in the evolution of influenza virus, particularly through the comparison of different virus types in different host species. By clarifying the mechanisms of influenza virus evolution, this work will help in generating the policies and strategies in epidemic prevention, vaccine selection and surveillance methods in long run. In particular, my thesis will address the following key questions: 1. What are the evolutionary patterns and processes of avian influenza viruses in wild aquatic birds? Are they in ?evolutionary stasis? as is often suggested? 2. How does the huge genetic diversity of AIV persist in wild aquatic birds? 3. How does Low Pathogenic Avian Influenza spread among migrating birds? 4. What are the evolutionary patterns and driving force of human influenza B viruses, and how do they relate to those of the more common influenza A virus?