Relative contributions of acrAB-tolC efflux and mutations in QRDRs, towards ciprofloxacin resistance in Shigellae were determined in the present study. Eight Shigella flexneri and six Shigella dysenteriae clinical isolates were included. Three consecutive mutants resistant to ciprofloxacin for S. flexneri SFM1 (≥0.25µg/ml), SFM2 (≥4µg/ml) and SFM3 (≥32µg/ml) were selected in 15 steps from susceptible isolate by serial exposure to increasing concentrations of nalidixic acid and ciprofloxacin. Similarly, two mutants for S. dysenteriae SDM1 (≥0.25µg/ml) and SDM2 (≥4µg/ml) were selected in 8 steps. The mutation frequencies for different steps varied in between 8.06-1.2 X 10-6. Mutations were observed in gyrA Ser83→Leu, Asp87→Asn/gly, Val196→Ala and in parC Phe93→Val, Ser80→Iso, Asp101→Glu and Asp110→Glu. Expression of efflux genes was measured using real-time PCR. Overall, acrA and acrB over-expression strongly correlated with fluoroquinolone resistance (p<0.05); while tolC and acrR expression levels did not. After disruption of efflux activity with CCCP, MICs for few ciprofloxacin resistant isolates were comparable to ciprofloxacin susceptible isolates. Overall, we established that fluoroquinolone resistance is end product of either a single or combination of mutations in QRDRs and/ or efflux activity. Also, we here report novel polymorphism at Val196→Ala in gyrA in clinical isolates and Phe93→Val, Asp101→Glu Asp110→Glu and in parC in majority of laboratory-grown mutants.