Escherichia coli Sequence Type (ST)101 is an emerging, multidrug resistant, extraintestinal pathogenic E. coli (ExPEC) clonal lineage associated with carbapenem resistance. As yet, there are no studies on the genome-wide distribution of methylation (the methylome) of this important ExPEC lineage. DNA methylation guides numerous biological processes including, genomic defence against foreign DNA, DNA replication and repair, gene expression and virulence. DNA methyltransferases (MTases) are frequently associated with mobile genetic elements (MGEs), which are important drivers of pathogenicity and antimicrobial resistance. In this study, we sequenced seven ST101 isolates using Pacific Biosciences (PacBio) Single Molecule Real Time Sequencing (SMRT) technology and determined the complete genomes of two isolates, and draft genomes of five isolates. SMRT sequencing generates primary sequence data and polymerase kinetics used to identify DNA methylation, allowing us to define the methylome and completely resolve all MGEs that encode active MTases. Additionally, using genomic comparisons with six publicly available ST101 draft genomes, we analysed the distribution of MTase genes across the ST101 lineage. Our analysis identified 13 putative MTases and ten DNA recognition sites, with five sites that have not been described previously. Furthermore, we identified a Type I MTase encoded within a Transposon 7-like Genomic Island and show that the acquisition of this additional MTase leads to functional differences in the methylome between two almost identical isolates. We show that the majority of MTases (n=10/13) are encoded on MGEs or ST101 specific regions, with variation in MTase distribution reflected by the MGE differences between genomes. It is well established that MGEs can contribute to the evolution of ExPEC due to their virulence and resistance gene repertoire. This study indicates the necessity for defining the methylome and genomic context of MTases and highlights the previously under appreciated role of MTases encoded on MGEs in ExPEC evolution.