Occurrences of newly emerging or re-emerging influenza viral infection present significant challenges to global public health. The causative virus, influenza type A and type B virus, is responsible for annual global epidemics and periodic pandemics. Continuing antigenic drift and genetic shift allow the emergence of new human strains of influenza virus. Therefore, it is critically important to understand the pattern of virus circulation and evolutionary in order to develop a plan for influenza control and prevention. In this dissertation, I analyzed patterns of viral circulation and evolutionary dy- namics for influenza A/H7N9 and influenza B using phylogenetic analysis and com- putational simulation. For influenza A/H7N9 virus, I performed Bayesian phylogeographic analysis to study the patterns of viral dissemination of low and highly pathogenic viruses isolated in China, and analyzed selection pressure, amino acid variations, and patterns of reassortment. This result revealed that although the two viruses evolve at similar rates, each possesses distinct evolutionary trend. Furthermore, I identified unparallel diffusion dynamics and mismatched spatial transmission predictor between these two viruses. For influenza B virus, I conducted phylodynamic analysis on two strains in the influenza B virus Victoria clade that are currently circulating, namely clade 1A.1 and clade 1A.3. I determined the transmission network unique to each virus and assessed amino acid variations that led to predominant circulation of clade 1A.3 virus in US during 2019-2020 season. I also identified possible co-assorting segments which may further stabilize viral fitness of clade 1A.3 virus. These novel findings presented likely aid in future control and prevention of in- fluenza A/H7N9 and Influenza B viruses.