Abstract: Objective Prophage is one of the mobile genetic elements carried on bacterial genome, which plays an important role in bacterial virulence and host adaptability. Phage-mediated serotype conversion occurs frequently, which brings inconvenience to the surveillance, diagnosis and prevention of Shigella. In order to explore the relationship between the serotype-converting phages of Shigella flexneri and genome evolution, we analyzed correlation between the distribution of prophage and the phylogenetic tree of Shigella flexneri. Methods In total of 294 Shigella flexneri with different serotypes from 17 provinces in China were selected. We compared the coverage of prophages and serotype-converting phages in the different genome of Shigella flexneri. Correlation analysis were did about the phage distribution in phylogenetic tree. Results The results showed that multiple kinds of prophages were carried by Shigella flexneri, and the same prophage may distributed in different serotype strains. Some strains carried bacteriophages without serotype-converting events. The bacteriophages appeared in clusters in the evolutionary tree, indicating a concentrated serotype-converting events. Conclusion We indicated the close relationship between serotype-converting phages and the evolution of Shigella flexneri. Our research is of great significant to prevent and control Shigella infection.