We investigated the molecular epidemiological characteristics of the Shigella flexneri strains primarily isolated in the provincial health center from 1998 to 1999. Among 289 isolates of s. flexneri, 270 isolates (93.4%) were confirmed as S. flexneri serotype 2a. The monthly isolation rate of S. flexneri strains was different from that of S. sonnei. S. flexneri strains were not isolated from July to August in 1998 but were isolated rarely during the same period in 1999. Shigella strains were isolated at higher rates in the areas of Chungbuk (64.4%), Busan (8.2%), Jeonnam (6.8%) in 1998 and in the areas of Busan (10.6%), Gangwon (9.3%), Gyeongnam (29.2%), Jeonbuk (4.2%) and Jeonnam (20.8%) in 1999. In these areas, the large outbreaks occurred with relatively high isolation rates of Shigella strain. Among 289 strains, 172 (59.5%) S. flexneri strains were isolated from female patients. Eighty-eight (30.4%) Shigella strains were isolated among the high risk age group of over 61 years. With the antimicrobial susceptibility tests, 284 isolates (98.3%) showed multiple resistance to more than four antibiotics, but all isolates were sensitive to ciprofloxacin, ceftriaxone and cefoxitin. We could divide on isolates into 5 groups (A, B, C, D and E) by analyzing PFGE patterns. Group A subdivided as 16 subgroups and 270 (93.4%) strains belong to the group A. The PFGE patterns of strains isolated from outbreaks revealed that the was only little difference corresponding one to three bands among strains. This result indicates that our isolates are genetically related.