Background: Multidrug-resistant Salmonella strains are now common globally, posing a serious healthcare threat. Aim: Identification of ciprofloxacin resistance with molecular detection of aac(6’)-Ib-cr gene in clinical isolates of Salmonella species. Methodology: A prospective, cross sectional & analytical study was conducted for a period of 12 months. Salmonella species identified from various clinical samples sent to the microbiology lab for culture were evaluated for ciprofloxacin using epsilometer test and Kirby Bauer’s disc diffusion method and and pefloxacin susceptibility using Kirby-Bauer’s disc diffusion method. Identification of aac(6’)-Ib-cr gene which is molecular marker for ciprofloxacin resistance was performed using real time polymerase chain reaction. Result: A total of 40 Salmonella species bacterial isolates were identified. Out of these, 39/40 (97%) isolates were resistant to ciprofloxacin using disc-diffusion and epsilometer strip methods. Pefloxacin resistance were seen in 34/40 (85%) bacterial isolates. The aac(6’)-Ib-cr gene was identified in 38/40(95%) bacterial isolates. Pearson Chi-square test indicated a statistical significant result with p<0.05. Conclusion: Pefloxacin can be used as surrogate marker for ciprofloxacin resistance in Salmonella species but with caution