Escherichia coli type three secretion system 2 (ETT2) is the second type of E. coli three secretory system. The complete ETT2 locus encodes 35 open reading frames (ORFs), while most E. coli have significant deletions and insertions in the ETT2 gene cluster. The intact ETT2 cluster or genes located in the ETT2 cluster contribute to the pathogenicity of avian pathogenic Escherichia coli (APEC). However, there are few reports on the genomic information and characteristics of ETT2 gene clusters. Here, we used whole-genome sequencing to analyze the characteristics of the ETT2 cluster and compared the types of ETT2 in this study with those reported previously. Compared with the ETT2 gene cluster in E. coli O157:H7, there were five different types of ETT2 in these strains. Strains possessing the complete ETT2 gene cluster maintained a closer affinity to those devoid of any genes from the ETT2 gene cluster. ST117 type predominated among these strains, and O166 was also adept at harboring an ETT2 cluster. However, no discernible correlation was discerned between the presence of the ETT2 gene cluster and virulence genes. This work will help researchers to understand ETT2 more comprehensively.