Streptococcus thermophilus is one of the most important starters in the dairy industry， with good fermentation characteristics. DNA methylation is a form of chemical modification of DNA that can affect gene expression without altering the DNA sequence. In this paper， two strains of Streptococcus thermophilus with large differences in acid-producing phenotype were selected as the research objects， and the relationship between m6A methylation and genetic phenotype was explored through methylome. The PacBio SMRT sequencing platform was used to sequence the genomes of Streptococcus thermophilus IMAU80278 and Streptococcus thermophilus IMAU20416 and measure the m6A methylation to compare the functional genes and m6A methylation differences between the two strains of Streptococcus thermophilus. The results showed that the genomes of Streptococcus thermophilus IMAU80278 and Streptococcus thermophilus IMAU20416 were similar， and the functional genes were mainly carbohydrate metabolism and amino acid metabolism. Streptococcus thermophilus IMAU80278 and Streptococcus thermophilus IMAU20416 showed significant differences in restriction modification systems， m6A methylation sites and m6A motifs， especially in the m6A methylation of genes related to carbohydrate metabolism and amino acid metabolism. It is speculated that the difference in m6A methylation may lead to the different acid-producing phenotypes between Streptococcus thermophilus IMAU80278 and Streptococcus thermophilus IMAU20416. In addition， this study explored the effect of Streptococcus thermophilus DNA methylation on fermentation characteristics from the perspective of epigenetics， and laid a theoretical foundation for the selection and utilization of excellent starter.