Epigenetic systems are important in bacteria, where DNA methylation is the most common epigenetic modification and is involved in genome defense, DNA replication, gene expression and virulence. Additionally, epigenetic systems are often associated with mobile genetic elements (MGEs), which form the accessory genome and are important in pathogenicity and evolution. Recently, we have defined the complete methylome of Escherichia coli strain EC958, a highly virulent uropathogen of the ST131 lineage, using Pacific Biosciences Single Molecule Real Time sequencing. Our analysis identified 11 methyltransferases (MTases), including 2 Type I and 1 Type IIG that have not been described previously. Using this data, we have analysed the MTase target site distribution within the genome of EC958 and examined the gene content of hyper- and hypo-methylated regions, with a focus on genes known to be regulated by methylation, including autotransporters and chaperone usher fimbriae. Bioinformatic analyses indicate that the distribution of MTase target sites significantly differs between the core and accessory genome of EC958. Specifically, a higher density of MTase target sites within MGEs were found to be associated with a Restriction Modification system comprising of two Type IIS MTases, which were previously defined as essential for EC958 growth1. In contrast, the MTase target sites associated with Dam are under-represented in the majority of MGEs compared to the core-genome. For Dam target sites, this difference in distribution is partially accounted for by large methylation-free regions (>= 1000 bp) that are associated with MGEs, which is suggestive of evolutionary pressure and selection against Dam methylation in MGEs. This is the first study to analyse the distribution of methylation across the genome of a uropathogen of the ST131 lineage and will help us elucidate the role of methylation in the regulation of uropathogenicity.