This study is a part of the surveillance study on childhood diarrhoea in the Andaman and Nicobar Islands; here we report the drug resistance pattern of recent isolates of Shigella spp. (2006–2011) obtained as part of that study and compare it with that of Shigella isolates obtained earlier during 2000–2005. During 2006–2011, stool samples from paediatric diarrhoea patients were collected and processed for isolation and identification of Shigella spp. Susceptibility to 22 antimicrobial drugs was tested and minimum inhibitory concentrations were determined for third-generation cephalosporins, quinolones, amoxicillin-clavulanic acid combinations and gentamicin. A wide spectrum of antibiotic resistance was observed in the Shigella strains obtained during 2006–2011. The proportions of resistant strains showed an increase from 2000–2005 to 2006–2011 in 20/22 antibiotics tested. The number of drug resistance patterns increased from 13 in 2000–2005 to 43 in 2006–2011. Resistance to newer generation fluoroquinolones, third-generation cephalosporins and augmentin, which was not observed during 2000–2005, appeared during 2006–2011. The frequency of resistance in Shigella isolates has increased substantially between 2000–2006 and 2006–2011, with a wide spectrum of resistance. At present, the option for antimicrobial therapy in shigellosis in Andaman is limited to a small number of drugs.