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The objective of this study was to assess the quantitative prevalence, antibiotic resistance, and molecular subtyping pattern of Campylobacter isolates from chicken and duck products from poultry slaughterhouses in South Korea. A total of 240 chicken (n = 120) and duck (n = 120) carcass samples collected from 12 poultry slaughterhouses between June 2014 and February 2015 in 12 South Korean cities was tested, and 131 samples were positive for Campylobacter. Duck samples showed a higher prevalence (P < 0.05; 93 out of 120) compared to chicken samples (38 out of 120), whereas Campylobacter cell populations from positives were lower (P < 0.05) in ducks (mean count: 183.8 CFU/mL) than in chicken samples (mean count: 499.7 CFU/mL). Most isolates were resistant to nalidixic acid (93.9%), ciprofloxacin (95.4%), tetracycline (72.5%), or enrofloxacin (88.5%), but only a few strains were resistant to chloramphenicol (0.8%) or erythromycin (3.1%). Most of the tested strains were classified into diverse pulsotypes according to repetitive element sequence-based-PCR banding patterns, indicating the diversity of Campylobacter isolates present in chicken and duck samples from poultry slaughterhouses. The emergence of Campylobacter contamination and antibiotic-resistant strains in food animals poses a potential risk to public health and should be regularly monitored for developing proper control measures.