Background: The natural hosts of Shigella are conventionally humans and other primates; however, the host range of Shigella has been shown to expand to many animals. Although Shigella is becoming a huge threat to animals, there is limited information on the genetic background of local strains. The purpose of this study was to assess the presence of virulence factors and the molecular characteristics of S. flexneri isolated from calves with diarrhea.Methods: From 2014 to 2016, 54 S. flexneri isolates were collected from diarrhea, and their biochemical characteristics were determined according to API20E and virulence factors via PCR. The molecular characteristics of the isolates were studied by MLST, MLVA and PFGE.Results: Fifty-four S. flexneri isolates possessed four typical biochemical characteristics of Shigella. The prevalences of ipaH, virA, ipaBCD, ial, sen, set1A, and set1B were 100%, 100%, 77.78%, 79.63%, 48.15% and 48.15%, respectively. None of the studied strains possessed the stx gene. Regarding the differences in virulence factor distributions, the 54 S. flexneri isolates fell into seven gene profile types. Among these VTs, VT4 and VT6 were the most common, accounting for 74.07% of all VTs. MLVA based on 8 VNTR loci discriminated the isolates into 39 different MTs, PFGE based on NotI digestion divided the 54 isolates into 31 PTs, and MLST based on 15 housekeeping genes differentiated the isolates into 7 STs, with 1 ST (ST227) being novel.Conclusion: Our findings provide baseline information on the distribution of virulence genes in and the molecular characteristics of S. flexneri collected from diarrheal calves, which is a potential threat to public safety. These data will be important for addressing clinical and epidemiological issues regarding Shigellosis.