The aim of this study was to determine the molecular mechanisms of fluoroquinolone resistance in E. coli isolated from cattle, goats, sheep, cats, and dogs in Turkey. Twenty nonreplicate E. coli isolates (chosen on the basis of RAPD pattern) from food-producing animals were selected for the study. To identify phenotypic differences between isolates, the sum of the MIC values of 14 antimicrobials was calculated; values ranged from 565 to 2520 mu g/mL, indicating the diversity in antimicrobial resistance present in the panel of isolates. PCR and qRT-PCR were used to characterize the presence and expression levels of known molecular mechanisms of fluoroquinolone resistance. The number of E. coli isolates having single, double, and triple topoisomerase mutations was 2, 10, and 5, respectively. Moreover, the number of qnrA -, qnrS -, oqxB -, and aac(6') Ib-cr-containing E. coli isolates was 1, 4, 1, and 17, respectively. Increased expression of acrB and soxS was detected in 2 and 9 isolates, respectively. The results of this study show a wide range of different mechanisms of fluoroquinolone resistance in E. coli isolates in Turkey.