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Rising concern about the use of antibiotics in food production has resulted in many studies on the occurrence of antibiotic resistance genes (ARGs) in animal-associated bacterial communities. There are few baseline data on the abundance of ARGs on farms where chickens are intensively raised with little or no use of antibiotics. This study used a high-throughput quantitative PCR array to survey two antibiotic-free chicken farms for the occurrence of ARGs and mobile genetic elements known to enhance the spread of ARGs. No antibiotics had been used on the study farms for five years prior to this study. The results provide a baseline for the occurrence of resistance genes in the chicken production system without direct selective pressure.Antibiotics 2020, 9, 120 2 of 12 cost-effective and efficient method to collect biomass representing a large population, and this has been used for monitoring the prevalence of pathogens in chicken flocks [8,9]. High-throughput quantitative PCR (HT-qPCR) and deep sequencing approaches have been used in a variety of human, animal and environmental samples to characterize the diversity of antibiotic resistance genes (ARGs) [10][11][12][13][14]. These methods are efficient and effective for the broad-spectrum detection and quantification of ARGs in complex samples.The aim of this study was to assess the presence and diversity of ARGs and mobile genetic elements (MGEs) in poultry farms that had not used antibiotics for 5 years. The WaferGen HT-qPCR system was used to detect and quantify ARGs and MGEs in environmental samples from two chicken farms. The PCR primers targeted ARGs of the major antibiotic classes, and integrases and transposase genes. Caged chicken sheds from two types of farms were selected for investigation; the first was an egg production enterprise which housed caged layer chickens (Farm L), while the second was a broiler breeder farm (Farm B). The results should provide useful baseline information regarding ARG prevalence in the chicken production system without direct selective pressure.