Shigella sonnei isolates from southwestern Korea during the epidemic periods of 1998 to 2000 were genetically related. The antimicrobial susceptibilities of the outbreak-related isolates changed annually. All isolates carried class 2 integrons, and the outbreak-related isolates from 1999 also carried class 1 integrons. The antimicrobial susceptibilities of S. sonnei isolates are readily changed by antibiotic selective pressures, and integrons are responsible for resistance to antimicrobial agents commonly used to treat shigellosis.