Introduction.Shigellosis remains a considerable public health concern in developing countries.Shigella flexneriandShigella sonneiare prevalent worldwide andS. sonneihas been replacingS. flexneri.Gap Statement.S. flexneristill causes outbreaks of shigellosis in northern Vietnam but limited information is available on its genetic characteristics.Aim.This study aimed to characterize the genetic characteristics ofS. flexneristrains from northern Vietnam.Methodology.This study used 17 isolates from eight incidents, collected in northern Vietnam between 2012 and 2016. The samples were subjected to whole genome sequencing, molecular serotyping, cluster analysis and identification of antimicrobial resistance genes. Additionally, phylogenetic analysis was performed including isolates from previous studies.Results.Clusters were identified according to spatiotemporal backgrounds. The results suggested that two incidents in Yen Bai province in 2015 and 2016 were derived from a very recent common ancestor. All isolates belonged to phylogroup (PG) 3, which was divided into two sub-lineages. Thirteen of 17 isolates, including those from the Yen Bai incidents, belonged to sub-lineage Sub-1 and were serotyped as 1a. The remaining four isolates belonged to sub-lineage Sub-2 and were the globally predominant serotype 2a. The Sub-1S. flexneriisolates possessed thegtrIgene, which encodes the glycosyl transferase that determines serotype 1a, with bacteriophage elements in the vicinity.Conclusion.This study revealed two PG3 sub-lineages ofS. flexneriin northern Vietnam, of which Sub-1 might be specific to the region.