Some species of the genus Komagataeibacter (formerly Gluconacetobacter) are involved in the industrial production of vinegar and they are the most resistant Acetobacteraceae to high acetic acid concentrations. During evolution, the genome of these microorganisms must have undergone mutations and rearrangements acquiring their intrinsic resistance to extreme environmental conditions such as high acetic acid and ethanol concentrations as well as low pH. In this work, Illumina and Pacific Biosciences (Pac Bio) sequencing technologies were used to obtain the genomic sequence of Komagataeibacter and Acetobacter pasteurianus strains. In silico analysis highlighted the main differences among A. pasteurianus strains and Komagataeibacter. Our results showed that the pan genomes of Komagataeibacter strains have around 900 additional CDS compared to A. pasteurianus. The core genome of Komagataeibacter strains compared in this study contains 1751 genes, 355 of which are not present in A. pasteurianus. Interestingly, Acetobacter strains possess amino acid and O-antigen exporter proteins that are absent in Komagataeibacter. These results confirm some of the past hypothesis and give new insights and directions to study acetic acid resistance. Additionally, the methylation state of three Komagataeibacter strains was analyzed by using Pacific Biosciences (Pac Bio) Single Molecule Real Time (SMRT) technology. This method offers also the capability to call two types of covalent base modifications, 6mA and 4mC, which allow us to perform the first methylome profiling for acetic acid bacteria. These data will provide indications on the gene regulation or DNA protection.