Abstract: Objective To study the distributions and genetic variations of Shigella resistance locus (SRL) and Tn7 multi-drug resistant genomic islands in dominant Shigella flexneri sequence type 91 (ST91) isolated in China. Methods The SRL and Tn7 of draft genome sequences of 59 S. flexneri isolates were compared with published complete genomes of S. flexneri 2002017 and YSH600. These 59 isolates covered 14 serotypes (1a7 isolates, 1b1 isolate, 1d1 isolate, 2a5 isolates, 2b1 isolate, 3a3 isolates, 3b1 isolate, 4a1 isolate, 4av1 isolate，4b1 isolate, X9 isolates, Xv25 isolates, Y2 isolates and Yv1 isolate)and 7 STs (ST9150 isolates, ST1091 isolate, ST183 isolates, ST1421 isolate, ST1431 isolate, ST1032 isolates and ST161 isolate). Results All 50 ST91 isolates, 1 ST109 isolate and 1 ST142 isolate each carried the SRL and Tn7 multi-drug resistant islands. 1 ST18 isolate carried only 3 resistant genes from two islands. The genes of the two resistant islands were not identified in the rest isolates. Insertion or deletions on SRL islands were observed in 9 ST91 isolate, as compared with genome of S. flexneri Xv 2002017, of which, 7 ST91 isolates deleted tetracycline resistance genes, 1 ST91 isolate deleted -lactamases oxa-1 gene and chloramphenicol acetyltransferase cat gene and 1 ST91 isolate had an insertion of -lactamase bla TEM-1 gene. No sequence variation was observed for Tn7 islands for all draft genomes analyzed in this study. Conclusion All of S. flexneri ST91 isolates analyzed in this study carried SRL and Tn7 multi-drug resistant islands. Moreover, genetic variations such as deletions and insertion were observed on the SRL island. The ST18 might play an important role in acquiring and spreading of the two multi-drug resistant islands, which was phylogenetically ancient as compared with ST91.