Wild aquatic birds are the natural reservoirs of avian influenza viruses (AIVs). It is estimated that 100 million seabirds live in the Antarctic Peninsula and adjacent islands, regularly encountering migratory birds that use the islands to nest. Between 2010 and 2013, we collected samples from 865 seabirds in Elephant, King George and Livingston islands, around Antarctica Peninsula: Chinstrap penguin (n = 143); Gentoo penguin (n = 208); Adelie penguin (n = 46); Brown skua (n = 90); cape petrel (n = 115); and southern giant petrel (n = 263). Serum (n = 673) samples were analyzed by competitive ELISA and swabs (n = 614) were tested by one step real-time RT-PCR for avian influenza virus (AIV). Sera from 30 chinstrap penguins, 76 Brown skuas and a single Adelie penguin were seropositive for AIV. Thirteen swab samples were AIV positive by RT-PCR, and complete genome sequences of H6N8 AIVs isolated from Brown skua and chinstrap penguin in 2011 were obtained. Phylogenetic analyses indicated that all gene segments of the H6N8 viruses were closely related to Argentinian and Chilean AIVs. The prevalence with which we identified evidence for AIVs infection in various Antarctic seabirds suggest viral circulation in Antarctic avifauna and interspecies viral transmission in the sub-Antarctic region.