As the human population and tourism increase in the Galápagos Islands, increased poultry production raises risks of pathogen spillover into native avian populations. Here, we characterize the disease risks to Galápagos avifauna of different types of poultry farming by comparing health status and serosurvey results between broiler and backyard chickens (Gallus gallus domesticus). Backyard chickens were more frequently diseased than broilers, and were more likely to be seropositive for several pathogens (Mycoplasma gallisepticum, infectious laryngotracheitis virus, infectious bronchitis virus, avian reovirus, and Marek's disease virus). Seroprevalence for other pathogens (avian paramyxovirus-1, infectious bursal disease, avian encephalomyelitis virus, and avian adenovirus) was relatively high among all chickens. Preliminary serological results from wild birds revealed no evidence of previous exposure to these diseases, which suggests that transmission of disease from poultry to wildlife is currently not detectable with the sample sizes and tests employed, and that wildlife are likely not the source of exposure to poultry. Our results suggest that backyard chickens may pose a greater threat to Galápagos avifauna because they are more likely to be infectious, have a high seroprevalence for numerous pathogens, and interact directly with wild birds or wild bird habitat, with no biosecurity measures employed. The broiler industry has greater potential for importation of pathogens into the islands and indirect transmission of diseases to wildlife (e.g., through use of poultry litter on agricultural land). Regulatory and management decisions should focus on minimizing the poultry–wildlife interface, reducing infectious diseases in backyard chickens, and preventing importation of poultry diseases.