H5N1 influenza virus is now endemic in many regions of the world. Outbreaks continue to occur with dev- astating impacts to the local economies and threatening human health. The transmission of the virus involves a complex interplay between the spatio-temporal dynamics of the potential avian hosts, the ecology of the virus and poultry farming and trade. Despite increased monitoring of wild bird populations and poultry trade, control measures remain insufficient to mitigate the spread of the virus. Here, focus is given on the influence of seasonality of migration and breeding in the transmission of H5N1. We also review recent findings on the interaction between migratory and local birds and poultry in the pattern of recurrence of H5N1 outbreaks. Finally, impacts of vaccination and co-circulation of avian influenza strains are discussed in the context of re-emergence and silent spreading of the disease.