The gene ccrM, encoding a cell cycle-regulated methyltransferase, which is well conserved among Alphaproteobacteria and plays a crucial role in regulating gene expression in the alphaproteobacterium Caulobacter crescentus. However, it remains uncertain whether CcrM-dependent methylation plays a similar role in other members of the Alphaproteobacteria, such as Brucella abortus. To explore the both the conservation and regulation of CcrM-dependent methylation in Alphaproteobacteria, Nanopore sequencing in tandem with recent machine-learning based algorithms were utilized to explore the methylomes of both Caulobacter crescentus and Brucella abortusunder a variety of genetic conditions. In Caulobacter crescentus, the results for wild-type demonstrating a strong correlation between Nanopore-based detection and previously published results. With confirmation of Nanopore’s validity, the study then measures the impact of Lon-mediated CcrM degradation on the epigenome, confirming that the deletion of lon leads to widespread changes in methylation. Whereas the removal of alkB, a potential demethylase, did not yield significant changes in global methylation during normal growth. Applying a similar pipeline to Brucella abortus led to the first report of global DNA methylation dynamics in this species and revealed that CcrM-dependent methylation was conserved among the two Alphaproteobacteria. In contrast to Caulobacter, the removal of lon in Brucella exhibited both species and chromosome specific effects on the genome. Finally, the study examined a ∆mucR strain in Brucella, revealing that, akin to recent findings in Caulobacter, the transcription factor MucR plays a conserved role in protecting methylation sites from CcrM activity.