This study investigated the effects of ciprofloxacin on specie and resistance of the bacteria isolated from the ducks reared in ciprofloxacin-present and ciprofloxacin-free duck population. Bacteria were isolated from the carcass swab samples collected from the slaughtered ducks. The result showed that the dominant bacteria isolated from the ducks were Macrococcus caseolyticus (M. caseolyticus), Staphylocuccus saprophyticus (S. saprophyticus), Enterococcus faecalis (E. faecalis) and Escherichia coli (E. coli). The minimum inhibitory concentrations (MICs) of ciprofloxacin against all isolates were measured, and the genes of topoisomerase II (DNA gyrase) and topoisomerase IV of S. saprophyticus, E. faecalis and E. coli were amplified and sequenced, respectively. The results showed that the site-directed mutations of DNA gyrase and topoisomerase IV of the above three bacteria caused the strains to generate high-level resistance to ciprofloxacin (MIC≥32 μg/ml). No plasmid-mediated quinolone resistance (PMQR) genes were detected. These results suggested that ciprofloxacin could affect bacterial species in the duck and induce bacterial resistance. Site-directed mutations of DNA gyrase and topoisomerase IV of S. saprophyticus, E. faecalis and E. coli were closely related to high-level ciprofloxacin resistance.