Backyard productive systems (BPS) are recognized as the most common form of animal production in the world. However, BPS frequently exhibit inherent biosecurity deficiencies, and could play a major role in the epidemiology of animal diseases and zoonoses. The aim of this study was to determine if influenza A viruses (IAV) were prevalent in backyard poultry and swine BPS in central Chile. Through active surveillance in Valparaiso and Metropolitan regions from 2012 - 2014, we found that influenza virus positivity by real-time RT-PCR (qRT-PCR) ranged from 0% during winter 2012-45.8% during fall 2014 at the farm level. We also obtained an H12 hemagglutinin (HA) sequence of wild bird origin from a domestic Muscovy duck (Cairina moschata), indicating spillover from wild birds into backyard poultry populations. Furthermore, a one-year sampling effort in 113 BPS in the Libertador Bernardo O´Higgins (LGB óHiggins) region showed that 12.6% of poultry and 2.4% of swine were positive for IAV by enzyme-linked immunosorbent assay (ELISA), indicative of previous exposure of farm animals to IAV. This study highlights the need for improved IAV surveillance in backyard populations given the close interaction between domestic animals, wild birds and people in these farms, particularly in an understudied region, like South America.