Trimethoprim-sulphamethoxazole (SXT) resistance increased among Shigella flexneri isolates in 1995 relative to previous years, in the Trakya region, the European part of Turkey. Since this region is the entrance to Turkey from northern countries, a heavy traffic of travellers passing through should have been importing or exporting the resistant isolates. We studied the genetic basis and epidemiology of this resistance and monitored the clonal changes which have taken place in the meanwhile. During the study period, a total of 70 Shigella spp. were isolated. Of these 58 were S. flexneri, 10 were S. sonnei and two were S. boydii. S. dysenteriae was not isolated. Of S. flexneri isolates 32 were SXT, ampicillin, chloramphenicol and tetracycline resistant (pattern I), while two isolates were found to be resistant only to SXT (Pattern II). Transconjugation experiments revealed that an approximately 80 Kbp self-transmissible plasmid carried the SXT resistance genes in both groups. However, EcoRI and HindIII restriction patterns of the plasmids from resistance pattern I and resistance pattern II were different. Ribotypes of three randomly selected isolates from pattern I were identical and were distinguishable from the ribotype of the isolate from pattern II. We concluded that at least two different clones with different plasmids and resistance patterns were spreading in our territory.