In recent years, with the rapid innovation and development of sequencing technology, researchers have tended to focus on DNA methylation research. DNA methylation is a way of regulating bacterial gene expression and altering the genetic performance without altering the DNA sequence. While a great deal of research has been conducted to understand the effect of eukaryotic DNA methylation on disease occurrence and plant growth, prokaryotic DNA methylation has barely been researched so far. For a better understanding of the current status of research on bacterial DNA methylation, herein, we briefly summarize recent developments in research on DNA methyltransferase and methylome in pathogenic bacteria and lactic acid bacteria and the techniques used to detect DNA methylation in order to provide a theoretical basis for the application of DNA methylation in lactic acid bacteria.