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<i>Escherichia coli</i> is classified into four major phylogenetic groups (A, B1, B2, and D) that are associated with antibiotic resistance genes. Although antibiotic-resistant <i>E. coli</i> is commonly detected in municipal wastewater, little is known about the relationship between the phylogenetic groups and antibiotic-resistant <i>E. coli</i> in wastewater. In this study, the survival of <i>E. coli</i> in wastewater and the changes to the relationships between each phylogroup and the antibiotic-resistant profiles of <i>E. coli</i> isolates from wastewater were investigated under aerobic conditions for 14 days. The isolates were classified into the phylogroups A, B1, B2, and D or others by multiplex PCR. In addition, the susceptibility of the isolates to 11 antibiotics was assessed with the minimum inhibitory concentration (MIC) assay. While <i>E. coli</i> counts decreased in the wastewater with time under aerobic conditions, the prevalence of phylogroup B2 had increased to 73% on day 14. Furthermore, the MIC assay revealed that the abundance of antibiotic-resistant <i>E. coli</i> also increased on day 14. After batch-mixing the experiments under aerobic conditions, the surviving antibiotic-resistant <i>E. coli</i> included mainly multidrug-resistant and beta-lactamase-producing isolates belonging to phylogroup B2. These results suggest that the phylogroup B2 isolates that have acquired antibiotic resistance had a high survivability in the treated wastewater.