The two multiple-antibiotic resistance (Mar) phenotypes (n = 8, respectively) and susceptible isolates (n = 4) of Shigella flexneri from China were characterized involving the efflux pump AcrAB-TolC. The accumulation of ciprofloxacin, acrAB-tolC PCR, and levels of mRNA with northern blots were performed in three groups. Sequencing of acrAB-tolC was performed in selected isolates. An efflux inhibition was performed with Phe-Arg-beta-naphthylamide. The accumulation of ciprofloxacin at steady state in susceptible isolates was significantly higher than that in the two Mar groups (p < 0.05). The level of accumulation in the Mar strains was increased upon the addition of the protonophore carbonyl cyanidem-chlorophenylhydrazone. The expression level of acrA mRNA in the Mar isolates was significantly higher than that in the susceptible isolates (p < 0.05). Mar strain H26 had a single-nucleotide substitution in locus 322(G-->T) of acrA, and Mar 0008 in locus 171(C-->A). The susceptible strain N15 had a base deletion in locus 36 (C) of tolC gene. The role of the inhibitors of efflux pumps was significant in some isolates with the high expression of Mar pump genes. In conclusion, overexpression of acrA gene leads to Mar in clinical isolates of S. flexneri, and ciprofloxacin acquired susceptible to S. flexneri with Phe-Arg-beta-naphthylamide.