DNA methylation plays various roles in bacteria and can contribute to bacterial interactions with their hosts, through diverse mechanisms such as genome maintenance or epigenetic regulations. The bacteria Xenorhabdus and Photorhabdus are pathogenic for insects and are found in the gut of soil with whom they are symbiotically associated. The roles of a conserved DNA-Methyltransferase (MTase) were investigated in these bacteria using deregulated strains and methylomic approaches. Great diversity was observed in the distribution of MTase-encoding genes, and a single MTase (Dam, for DNA-adenine MTase) was identified in all the species of these two genera. Methylome analysis showed that the GATC motifs recognized by Dam reached a high methylation rate (>99%) in the studied strains. Enrichment of unmethylated motifs in promoter regions was observed and may reveal mechanisms of epigenetic regulation. The Dam overexpression was associated with a reduced swimming motility, caused by a downregulation of flagellar genes, in both Xenorhabdus and Photorhabdus. In contrast, alteration of various major phenotypes such as hemolysis or virulence depended on the species studied. Our work revealed the diverse roles played by a conserved DNA MTase during the life cycle of entomopathogenic bacteria.