We report the sequence of the quinolone resistance-determining region of the gyrA genes of either susceptible or low-level-resistant clinical isolates of Coxiella burnetii. The sequences of low-level (MICs, 4 micrograms/ml) and high-level (MICs, 8 and 16 micrograms/ml) resistant strains stepwise selected in vitro were also determined. The gene sequences of all of the clinical isolates and that of the in vitro-selected low-level-resistant strain were identical. Sequence analysis of the in vitro-selected high-level-resistant strain revealed a nucleotide mutation leading to an amino acid substitution of Gly in place of Glu at position 87 of the GyrA amino acid sequence. These results indicate that high-level resistance to ciprofloxacin is associated with a nucleotide mutation in gyrA, whereas low-level resistance to quinolones is not.