Wild birds are the major reservoir hosts for influenza A viruses (AIVs) and have been implicated in the emergence of pandemic events in livestock and the human population. Understanding how AIVs spread within and across continents is critical to develop successful strategies to manage and reduce the impact of influenza outbreaks. In North America, many bird species undergo seasonal movements along the North-South axis, hence fostering opportunities for viruses to spread over long distances. To assess the relative contribution of bird migration along flyways, we undertook a large-scale phylogeography analysis of AIVs sampled in the USA and Canada. We developed a genetic algorithm for the maximum likelihood estimation of highly dimensional models. Based on phylogenies reconstructed from nucleotide data sets, our results show that migration rates within flyways of AIVs are significantly higher than between flyways, suggesting that migratory birds are an important driver for the dispersal of avian influenza viruses. These findings provide valuable insight on the maintenance and transmission of AIVs, hence allowing the development of improved surveillance and risk assessment programs.