Influenza (flu) is a common infectious disease, but it is unusual in that the primary timescales for disease dynamics (epidemics) and viral evolution (new variants) are roughly the same. Recently, extraordinarily reliable phylogenetic reconstructions of flu virus evolution have been made using samples from both extant and extinct strains. In addition, because of their public health importance, flu epidemics have been monitored throughout the period over which the phylogenetic trees extend. In parallel with this empirical work, theoretical ecologists have developed mathematical and computational models that elucidate many properties of multistrain systems. In the future, to unravel and interpret the complex interactions between ecological and evolutionary forces on flu dynamics, the documented evolution of the virus must be related to the observed population dynamics of the disease. New theoretical insights are also required to simplify model structures and facilitate predictions that can be tested with accessible data.Annual influenza epidemics, and occasionally devastating pandemics, raise deep ecological and evolutionary questions that are only beginning to be appreciated and explored.