This study was set up to assess the patterns of antimicrobial susceptibility and mutations in acrA-tolC genes of Shigella isolates and its association. One hundred and three isolates of Shigella spp. were tested to evaluate the antimicrobial susceptibility and mutation on acrA and tolC genes. The antimicrobial resistance profiles were: tetracycline (99%), ampicillin (85.4%), chloramphenicol (83.5%), trimethoprim (85.4%), ciprofloxacin (25.2%), cefazolin (3.9%), cefotaxime (3.9%), and gentamicin (2.9%). The rate of mutation in tolC was 90% (S. flexneri) and 30.8% (S. sonnei). Shigella flexneri isolates were more resistant than those of Shigella sonnei to chloramphenicol (97.8 versus 0.0%, p<0.001) and ciprofloxacin (27.8 versus 7.7%, p= 0.106). High frequency of mutation was found in gene tolC (82.5%), but relatively less in acrA (22.3%). Shigella flexneri isolates were more mutated in tolC gene than S. sonnei (90 versus 30.8%, p<0.001). Our study suggested that mutation of acrA and tolC may play major role in multiple antimicrobial resistance in Shigella spp. Shigella isolates are emerging which are resistant to first and third generation cephalosporin like cefazolin and cefotaxime, which is a matter of concern in terms of shigellosis treatment.