Shigella, an enteric pathogen, causes widespread bacillary dysentery around the world. Over the past few years, the emergence of resistance to multiple antimicrobials and new serotypes has brought new challenges to the surveillance and prevention of Shigella. The rapid development of genomics contributes to a better understanding of origins, mechanisms of variation and spreading principles, and has great scientific significance to control the spread of bacillary dysentery. From the perspective of genetic source, this essay focuses on the evolutionary relationship between Shigella and E. coli, as well as the possible molecular mechanisms. For the purpose of providing reference for researching and prevention of Shigella, the article also outlines the advances on genome evolution of S. flexneri, S. sonnei and S. dysentery type 1 with a detailed description of their features on temporal and spatial distribution and of the function of variation in resistance genes during evolution.