Infectious diseases have the potential to cause rapid decline and extinction in vertebrate population and are likely to be spreading with increased globalisation and climate warming. In the Southern Ocean and in Antarctica no major outbreaks of infectious diseases have been reported, perhaps because of isolation and cold climate, although recent evidence suggest their presence. The major threat for the Southern Ocean environment is today considered to be fishing activities, and especially controversial long-lining that is assumed to be the cause for the major decline of albatrosses and petrels observed recently. Here we show that two highly pathogenic diseases (worldwide spreading avian cholera, Erysipelas bacteria) are the major cause of the decline on Amsterdam Island of the large yellow-nosed albatross population that was previously attributed to long-line fishing. The diseases are affecting mainly chicks during their first weeks of life with a cyclic pattern between years, but also adult birds that can be found dead on the colonies. The outbreak of the disease occurred probably in the mid 1980s when the population started to crash at the same time that chick mortality increased and adult survival declined. The diseases could today threatening of complete extinction the very rare Amsterdam albatross, and are probably also affecting sooty albatrosses. The spread of diseases in the remotest areas of the world raises major concern for the conservation of the Southern Ocean environment.