Repeated outbreaks in epidemic areas and invasion of new countries and regions expanded influence on poultry production, economics and the ecology of wild birds. Highly pathogenic avian influenza (HPAI) H5N1 has moved the world closer to a further global pandemic. An understanding of HPAI H5N1 transmission and persistence is therefore of significance for the prevention and control of epidemics. In this review we consider virus movement through poultry production systems (live bird markets, small holder farms and industry), wild bird migration and vector media (biological and mechanical); risk factors in poultry production systems (commercial, backyard and free-grazing farm); and the ecological environments (avian community, ecology and geographical isolation) of epidemic areas, and their effects on H5N1 virus transmission and persistence. We conclude that the pandemic potential, widespread transmission and sustained persistence of H5N1 is the result of conflicts between traditional production and consumption habits and the intense poultry production industry in Southeast Asia.