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Background To investigate fluoroquinolone resistance and associated mechanisms of Shigella sonnei isolates in Jiangsu Province of China between 2002 and 2011. Methods All 337 unduplicated S. sonnei isolates were collected from hospitals in Jiangsu Province from January 2002 to December 2011. Fluoroquinolone susceptibility was characterized by Kirby-Bauer disk diffusion method, and direct nucleotide sequencing of genes of the quinolone resistance determining regions were conducted. Also, the transferable quinolone resistance determinants, including qnrA , qnrB , qnrC , qnrD , qnrS , aac-(6′)-Ib-cr and qepA were amplified by PCR. Results Among 950 Shigella isolates, 337 (35.5%) were identified as S. sonnei , of which 76.6% displayed nalidixic acid resistance and norfloxacin-resistant isolates appeared in 2005-2009, with an average resistance rate of 21.8%. Commonly reported point mutations of Ser83Leu and Asp87Asn/Gly in gyrA and Ser80Ile in parC were detected, with mutation rates of 78.0%, 9.5% and 30.3%, respectively, while no alteration in gyrB or parE were detected. Besides, His211Tyr mutation in gyrA was first reported in a S. sonnei strain in 2009 and two novel mutations in parC were found, of which Met86Trp occurred in another strain in 2009 and Ser129Pro appeared every year except 2011 (28.8%). Plasmid-mediated quinolone resistance determinants were found in 23 isolates and 19 of these isolates were resistant to both nalidixic acid and norfloxacin. qnrB , qnrS , aac-(6′)-Ib-cr and qepA were detected in 1, 7, 14 and 2 S. sonnei strains, relatively, and the most abundant PMQR gene found in this work was aac-(6′)-Ib-cr (4.2%). Interpretation & conclusions S. sonnei became increasingly important as fluoroquinolone-resistant isolates emerged, and further detection on the resistant genes would be useful in the treatment and control of this infection. [ABSTRACT FROM AUTHOR]